Okay, time for me to weigh in, a question like this practically invites me. Unfortunately this is difficult to answer without far more information about your world, and in particular what you have done to justify humans fighters instead of AI or missles being used.
For this answer I'm starting with a key assumption, high G manuvers are common. This seams likely in a close combat battle unless you go out of your way to prevent it. Much of this question is potentially invalidated if you remove high G meanuvers, either by making it too costly in terms of fuel, adding innertial dampeners, or some more complex handwave such as my claim that shields worked best with low acceleration thrusters.
This answer also presumes a number of thrusters on a ship. If you limit the ship to only say 3 thrusters or had a primary thruster that was stronger then the others (both plausible for cost reasons, it may be cheaper to make fewer thrusters or lowe output thrusters an demend economical to trade off less meanuverable crafts for the ability to make more) then this answer may be invalidated. If the number of thrusters is limitd enough the control scheme could change, but this answer still is quite likely. If there is a single thruster with more output then others then that defines your 'forward' and this could redefine much of the answer.
Where should the pilot face
the pilot would presumably would reside within a control hub orb at the center of the craft. This orb rotates so the pilot is best positioned to tolerates the G forces associated with acceleration (see Low-tech inertial dampener options ) This rotation is automatic and the pilot doesn't control it. The primary motivation is simply to allow the pilot to survive higher G forces by positioning his body in the most optimal position to endure the force.
In fact to prevent the pilot from crushing himself with G forces, while still allowing him the ability to make use of all acceleration he can handle, the craft would likely have some sophisticated soft (non-intellegent, just well programmed) AI that considers the pilots position before deciding how large a thrust to exert. The pilot will not be allowed to achieve 'maximum acceleration' when his body is in the wrong position because max acceleration would kill him. Instead he can only accelerate up to some acceptable G force, and then as his body rotates into a better position the maximum acceleration allowed to achieved in that direction will be increased since the computer determines the pilot can now survive that level of G force.
This is all done purely to protect the pilot, but as a side effect the pilot now has a very clear orientation. The direction(s) he is currently accelerating towards are 'forward' to the pilot. Keep in mind that the pilot will sense his 'forward' as being the combination of all forces on him, he may have three fruster firing at different directions & rates to propell him, but his sense of 'forward' will be the vectoral sum of the acceleration created by those thrusters.
In the case that the pilot is not accelerating at all then 'forward' will be defined as the last direction the pilot was accelerating towards. The pilot may have an option to override his 'default orientation' in situations of no (or very little) acceleration for his own covenience, such that he is looking the direction that he is most interested in looking, but during the heat of combat when he will constantly be accelerating in differnt directions he will always be using his acceleration direction as his default 'forward'. From a programing perspective likely he can set his default forward if acceleration is uner 1 G but the moment he experiences more then 1 G worth of acceleration the computer will immediately revert him to 'acceleration=forward' mode which is the prefered mode for heavy movment or combat.
Eyes in the back of my head (and top, and bottom...)
Now that we have a forward, how will it be displayed to the pilot? Most likely he will have a 180 x 180 (so up & down as well as 2 D plane) degree display, either actuall screens on the wall or more likely some sort of headgear that displays the screens infront of his eyes. He will likely have his screens split such that half his screens are 'forward facing' and half are 'aft facing', so he can see all degrees of the sphere by changing which screen he looks at. Actually the screens would likely be configurable and allow him to do things such as making his aft or fore screen view larger or break up more screens depending on his needs, one sign of a good pilot would be being able to modify his screens to give him the most 'optimal' view for him and each pilot may have a different prefered display, in much the same way that people playin MMOs may have widly different screens as they install and remove addons to configure their display to display information in a way they prefer. The point though is that he will have the overlay to display everything.
This overlay will constantly adjust his view as he is rotated due to changes in acceleration, to keep the center of his fore display facing the 'forward' direction (ie the way he is accelerating).
Actually, there is a slight translation time here. He can't be instentaniously rotated towards a new point acceleration (there is some time from when he starts firing his port thrusters and when he is rotated within his cockpit so his port frusters are now his aft thrusters). It would also be confusing to have the screen transition immediately to show a different point of view as 'forward' to the pilot, he needs to watch the screen rotate to a new 'forward' direction so he knows where something relevant (like an fighter craft he is chasing) is relative to his new 'forward'. These two issues work nicely together though.
Presumably when he starts to accelerate in a new direction both his physical body and the screens sense of 'forward' will be rotated at the same time. He will see the screen rotating as he 'feels' the rotation, this will help to keep his orientation during the transition between the 'old' forward and the 'new' forward. While he is rotating his tactical display will likely depict an icon (and possible an 'arrow' along with it) that will show him where his new forward is (ie where he is rotating to face) with the icon rotating towards the center of his vision as he is adjusted towards the new forward.
The Enemy's gate is wherever it happens to be
Notice this makes direction entirely relative, there is no absolute direction, I can't tell you that the enemy gate is down with this approach. The enemy gate was fore a minute ago, now it's aft, sone it's port/fore/up etc. I don't consider this a problem. You don't really care about an aboslute position, all you care about is where you are relative to key tactical points and/or threats.
If were assuming a hectic close range space battle (again, probably not realistic in real life, but implied to be the case in your world) then things are changing all the time. Enemy crafts are moving around you, they are never at the same place twice. Unlike Ender's game there was no final destination you're headed to and that your done once you reach. You may think of your enemy capital ships as 'down', but your fight isn't over just because you reach them, your just fly past them and rotate around for another pass at them after all. Nothing is really 'down'. All you care about is where you are relative to the things you want to be relative to.
This information is better served with a good tactical display! You already are being provided some semibalance of a 360 degree display, so if you want to know where a gigantic capital ship is just look, it should take a split second to identify it in your display. To make it even faster (because in combat split seconds matter) your have more complex targeting and tactical displays overlaying your 360 HUD. You could arrange for a little colored arrow to be projected from the 'center' of your screen in the direction of key locations you care about, like your home ship and the enemy capital ship your attempting to bomb, so you know what direction to look to find them. You can toggle targets to have them lit up on your screen and similar color coded lines to show where they are. A tactial display showing you what direction your relevant points of interest are is more useful. In a sense you can have multuple 'enemy gates', ie points of tactical importance you want to always be aware of the location of, at one time.
The enemy gate is also at starpoint 125x234x3
Okay, so there likely is also an absolute direction that is predefined by every fighter's computers. This can be used for a pilot to communicate concepts such as "fighter inboud as 6 oclock " in a method that has meaning to other pilots. This coordinate system would likely be mostly invisible to the pilots though, instead of trying to figure out actual cooridnates they would ping some location on their map and their com system would relay the location to other's maps and simply know where to ping relative to the pilots sense of forward. Alternatively some third party would be feeding updated tactical information. So yes there is a way to give absolute direction, but it's not something a pilot needs to think about or consider in the heat of combat.
that's one funny looking steering wheel
I haven't said it explicitly, but al controlls would transition at the same rate that the pilot own vision was rotating. If he pushes the fore control his thrusters will push to move him in the direction he is currently 'facing' in his display, whatever that direction is. As his display rotates towards a new 'forward' his controlls will adjust their definition of what 'fore' is accordingly.
So how does the pilot use this display to steer? That's a more complicated question. Other's have suggested joysticks, trackbars, etc, they won't help. All the control schemes we currently use as human only really work for two demetions, not three. The 3 dimentional control scheme I can think of would litterally measure a hand's motion in 3 dimentions, but doesn't work well as soon as a force can cause the hand to move when not intended (ie, when you suddenly have 4 G of force pushing you down because you had to duck under an incoming missle and you can't suspend your hand as easily under that force).
As such I don't think a single control scheme can be used. I think we need two control schemes, utilizing your equivlent of a joystick for controlling two dimentions, but having two of them to combine to allow control of all 3 dimentions at once. To put it more simply, one joystick for each hand. So which directon does each joystick control?
I spoke about our sense of acceleration as being a single senes that tells us exactly what direction were traveling...but I lied. We actually have effectively two senses for acceleration, our sense of up & down is rather different then the others. In particular our sense of 'down' is far more accute, due to the major plummitting sensation in our stomach we get the moment we have more then 1 G of force facing down. As such if we have a two controll scheme it makes sense to have those controlls be one for the standard 2 d plane and a second for 'up' and 'down' plane, combining to allow controlling all four planes.
Were facing war, you must respect the gavity of this situation
full 3 D space flight, particularly with such heavy accelerations as I anticipate in space, suggest a new wrinkle withour controll systems. At any time you may be experiencing multuple G worth of force pushing in any direction. This means that no matter how you lay out your controlls it's possible that your pilot may have heavy G forces pushing the pilot's hand 'down', ie making the pilot push his controlls in a direction he doesn't want to because he can't hold his hand steady agains the G force he faces.
This situation doesn't happen in a fighter jet as much, but the pilot only risks facing high G in one direction at a time, and the controls can be adjusted accordingly. facing high G from any number of different directions at once is much harder to handle.
At the very least the pilot's craft will have to adjust partially for this. If the pilot is likely to face heavy G pushing his hand in a direction decrease the sensitivity of the controller (or even have the controlls actually 'push back' against his hand harder) by an according amount so that his pushing harder on the controller does not actually cause the controller to register that as a request to move faster in the stated direction.
Some other approaches, such as having the two different joysticks reside on perpendicular plans from each other, could also be used to address this, but I won't get into the subject much more then to suggest the possibility.
Your pulling me in multuple directions
One last hurdle to driving is the competing need to move in different directions at different accelerations. Remember, the pilot can only accept G forces up to a certain degree before they render him unable to fly, and, more importantly, the degree of G force he can tolerate is dependent on orientation of the force. He can survive g forces directed 'down' much better the ones directed 'up' for example. For this reason I suggested that the ship control the maximum g force allowed based of off the direction the pilot was facing.
This brings up an intresting question for how we define what it means to push our joystick as far forward as it can, ie we say we want to accelerate as fast as possible. Since 'as fast as possible' is different depending on direction were headed it can have odd implications. Imagine I push my joystick as far as it would go in a 45 degree angle, intuitively saying "I want to go as fast as possible in the fore and starbord directions" I can survive acceleration in the fore direction that are much higher then the starboard. Do I accelerate as fast as I can handle in each direction, meaning I don't accelerate diagonally as I might assume, but instead in a direciton that is far more fore then starbord? or do I limit my maximum acceleration fore so that I'm accelerating both fore and starbord at the same rate? The former seems confusing, the latter could get me killed if I'm trying to dodge a missle and my computer won't let me move as fast as I theoretically could to avoid it.
I believe thta the controlls always work like the later example, accelerating at the maximum allowed rate for each direction even if that means I accelerate faster in one direction then the other. However, a pedal (or other control) will likely exist to allow me to instead 'correlate' the directions, so that my acceleration is based off of the maximum acceleration in whichever direction I can least tolerate acceleration in. So basically the can toggle between most acceleration and more 'controllable' acceleration. If this were a pedel they would even get a degree of control between 'completely correlate these two directions' and 'don't correlate at all'. Though you could argue the inverse, where directions are usually correlated and a pedal allows maximum acceleration in any direction instead, as being the default. The key point is the likely can alter the control schemes.
I tend to put on weight when stressed
Again the computer is trusted to decide 'maximum allowable acceleration', but what is that? Humans can high g forces for short term that they can't survive over a long term. In addition a human who has been experiencing a high sustained G force for awhile may be stressed and less capable of surviving a suddent short term higher G force in another direction, even if they could have survived that under other more ideal situations, and of course some pilots can simply endure higher threasholds then others.
If we assume thrust is cheap (which it is if your having highly meanuverable crafts at all....) then the craft will likely be designed to allow thrust up to the max a human can survive even for short times, to allow more meanuvability. But the computer may not allow someone to try to travel at that for sustained periods.
I imagine there would be a(nother?) pedal that is the "Oh $%!#" pedal, this is the one that says the pilot needs to accelerate now no matter what to get out of the way of something. This pedal would loosen the definition of 'maximum' acceleration to allow higher G forces to be experienced by the pilot. When the pilot is willing to risk temporary high g to do a meanuvour he presses this pedal to allow it, but the pilot can't accidentally go so fast that he knocks himself unconcious unless he has pressed this pedal, it's the laxing of his own safety procedures when he judges it necessary. This is definately a pedal to allow more nuainced control of just how much 'extra' G force to allow, a slight press on the pedal may simply mean "I want to go at a higher sustained G then usual, but nothing dangerous" while a full press on the pedal says "I'm willing to pass out half a second from now because that's the only way to avoid coliding with a friendly fighter and killing both us.
This is war, man up!
Now an aside, the most realistic is that your fighter craft will have at least two men in them, much like modern fighters. This frees your pilot up to use him hands entirely for steering, no taking his hands off the controls for anything else.
This is relevant becuase my controll scheme has the pilots hands busy at all times. While this scheme can work with a single pilot it works far better if a second person was in the fighter handling controlls that the pilot can't afford to worry about while focusing all his energy on driving. Driving will be harder here, requiring paying attention to multuple angles and fighting the G forces to keep your hands on the controllers right etc, so the pilot won't be able to afford as much attention to other activities as moder fighter jet pilots can either.
A sophesticated AI, especially if combined with audio input to controll less-critical systems, could likewise help here if you don't want a second pilot.
If you have a single pilot expect the 'joysticks' the pilot uses to be very complex with many controls built around the joystic to be toggleable with button presses. Though only so many things can be on a joystick, some controlls must be placed moer out of the way to avoid accidental activation.
Shooting down some suggestions
Now lets address the related question of aiming the guns, which has been brought up We are already more then capable of writing a soft Ai capable of aiming a turret gun at a moving target with more accuracy then a human pilot ever could. Furthermore, it would take too much focus for a pilot to focus on both aiming and moving, one act would distract from the other. As such the logical option is that a soft (Ie, not intellegent, just well programmed) AI would be responsible for fireing. This has the added advantage of allowing firing at multuple targets at once, making full use of every turret despite the pilot only being able to look at one at a time.
Unfortunately it's also boringly practical, it doesn't feel like an interesting space battle if your only job is to drive and trust your computer to kill everything. It also makes your pilot feel rather worthless and just reiterates the idea that humans don't belong in space fighters, which is something you've clearly implied you want to make happen.
One option is to say that there are only so many guns on the sphere, that they can only cover certain angles of fire, and possibly that they have a slow recharge time before being ready to fire again. This places more tactical challenge on the pilot. He won't be aiming exaclty, but his job is to make sure an enemy is within range of the turrets that are ready to fire.
This would give a feel much like navel battle where one didn't so much 'aim' their cannons as they focused on trying to 'cross the T' to arrange for their cannons to be facing in the general direction of the enemy while the enemy wasn't facing them and trust the cannons to fire. The tactics are all about knowing where you want to position yourself to ensure a shot can be fired, and even more so knowing where your enemy wants you and not being in those spots. A skill pilot may even notice that the enemy just fired from his aft cannon and that there will be a X second recharge before that cannon is ready to fire again and thus he can move in for an easy kill while one of the gunns is unable to cover the pilots flank etc.
Alternatively you could add a second man in charge of acting as a gunner (there is no way the pilot can fly well and shoot well in this scenario, not unless you greatly limit both number of guns and thrusters). If so they gunner will likely have a setup similar to the one for the pilot, except that in addition to the usual 360 display he has the ability to toggle which 'gun' he wishes to control and he gets a zoomed in display with that gun but...well it really takes allot of work to justify having humans gunning and the solution for how/why the humans are aiming in this case depends largely on what handwave excuse you used to justify guns being mained by a pilot.