There are some very deeply rooted, age-old issues behind your question. In a nutshell they all boil down to: How do interstellar travelers navigate among the stars? Let's take a look at this question in depth, and then we can see about answering your specific question.
So how do people on EARTH navigate, anyway? Well, thanks to generations of people who were either very bored or very curious, humanity has a strong collective grasp of exactly where the Earth is located within the solar system, and exactly what we can expect the night sky (and day sky) to look like at any given time on any given day. This is key to navigation. Using a sextant and any one of a set of Navigational Stars (or the sun, moon, or planets) a navigator can determine his/her exact location on the surface of the Earth. The positions of satellites in orbit are monitored by tracking stations at fixed, known location all over the Earth whose positions are accurately determined using stellar navigation. The GPS would not be able to function without these tracking stations, since their positions would decay over time. The tracking stations are able to monitor and adjust the orbits of the GPS satellites, since the positions of the tracking stations never vary, but remember that their position could never have been determined without first using the stars to get a bearing. No matter how advanced the navigation technique, a map of the sky is needed to take bearings.
Something to remember is that the mapping of the sky around the Earth has taken literally thousands of years. Methods have become more sophisticated and technology more advanced, but the core of knowledge was still gained through prolonged observation and experience. This is presumably something our intrepid interstellar explorers will not have.
Luckily, thanks to a nifty phenomenon called Stellar Parallax, we humans have managed to map the stars beyond our solar system to a startling degree of accuracy. Unfortunately, this method has a limited range. Presumably as science marches on we will produce more and more accurate maps and longer and longer ranges, but as it stands we can currently only take accurate parallax measurements to a distance of ~1600 ly. This might sound like a lot (and it really is pretty damn far) but the galaxy is a very vast place. Our maps cover about 0.07% of the Milky Way Galaxy. That's not terribly encouraging, but for now let's just focus on what we do have mapped.
So let's say we have someone who is really bored, really rich, and really sick of people. They hop in star ship and blast off at FTL speeds (#magic) and makes it to Polaris, which is about 433 ly away. But what now? Our explorer is too far away from Sol to use accepted sky maps. Stars will be in different positions in the sky thanks to parallax, since our explorer is so far from home. Luckily, our star charts cover this area, and with a bit of extrapolation our explorer can predict what the sky will look like in the Polaris system just from our knowledge of where the stars lay with respect to the Sun. If the ship has a powerful enough telescope, our explorer can use his current navigational data to orient himself in Polaris and start mapping more distant stars using more parallax. This might take some time, but it will both increase the accuracy of current star map and sky map and extend the current star map past what is currently achievable from Earth.
Next our explorer will want to start mapping the planet (I assume he found a planet upon which he wants to settle). In an empty vacuum it would be very tough to chart a planet's orbit, but our explorer has luckily already mapped out the sky using his extrapolated parallax data. Using these stars as a reference, our explorer can watch the planet(s) and sun(s) and moon(s) and get a pretty accurate picture of the system of orbits, including critical data like eccentricity, inclination, etc. Combining this new data with the sky map can produce an almanac of useable navigational points in the sky including stars, planets, moons, suns, and possibly other alien objects. It is imperative, however, that this process goes in this order. Trying to map the planetary orbits without first mapping the sky will result in failure.
Now that we have an almanac of navigation points our explorer can navigate the star system to his heart's content. Tracking stations can be placed on the surface of the planet using stellar navigation similar to that used on Earth, only with an alien sky and alien navigation points. These tracking stations, being permanent references, can be used to further deploy more navigation equipment like GPS satellites or the like. Now our explorer can move on to another star system and repeat the process for as long as there is predictable parallax data from which to pull.
Now for the fun part: bombing stuff. In the best case scenario (for bombing, that is) the planet over which the war is being fought is populated, the sky map is well documented, tracking stations are in place, and orbit data is very accurate. In this case orbital strikes can be calculated down to the tens of centimeter (that is not an exaggeration; we can almost do that right now on Earth with missiles). This is, of course, utilizing every available resource from ground station data to GPS satellites to visual rangefinding. In less optimistic situations the battleships will likely have at least some combination of above resources from which to draw. This will limit accuracy somewhat, but if there is a sky map and available orbital data then strikes are possible no matter what. In the worst case scenario where a battlefleet must fight in an unmapped system there will be considerable difficulty even hitting the correct continent. Sky mapping and orbital analyses will be fairly critical for accurate strikes against ground targets.
That being said, all of the above assumes the use of fairly modern navigational methods. It is entirely possible that as science marches on technology will allow for accurate machine vision enabled computers that can orient a ship in orbit without any sort of sky map. A sky map would still help, of course, but in a pinch such a computer might be able to put the hurt on a target even without in-depth star mapping and orbit analysis. High power telescopes and accurate laser weaponry would also need no navigational data to hit a target in visual range. Just point and shoot so to speak. Technology may also allow for very fast mapping of the sky and orbit analysis. Current methods would take months to accomplish this with any guarantee of accuracy, but delicate enough sensors could perhaps give accurate data in minutes or even seconds, making the entire process effectively instantaneous.
I would say that given any reliably effective method of travel between star systems, there will also be an equally effective method of navigation to ensure star ships can get from place to place. Mapping is also the first thing anyone will likely do upon entering a star system for the first time, so unless there is literally no time at all to get one's bearings, it will probably be simple enough to warp into a system (or whatever method of FTL you prefer), map out the sky and any planetary orbits, and then commence with the mission, whatever it is. If mapping is truly daunting, then I would personally sent unmanned mapping probes far ahead of my colonists and military forces to ensure some data is gathered and waiting if I enter an unknown system.
I hope I've helped some. Good luck!