Your first point is great. Spacecraft that are laid out as if there's a "down" that's perpendicular to the direction of thrust are almost always a stupid design and a holdover from depictions of spacecraft as essentially just aircraft or naval ships. So yes, laying the ship out as a stack of consecutive floors, sort of like a skyscraper, is objectively the best design for this kind of spacecraft. However, you've got a couple of issues here.
1. You're going to need a way to store that antimatter.
Your antimatter is, for some reason, in the form of anti-bismuth. OK, the first thing we're going to need to do is to give it an electric charge. We can't just hold it in a tank made of matter, because as soon as it touches the walls, your solar system gets a temporary second sun. So we need some way to hold it in our ship without ever touching it. Luckily, there is a way to do that (although it only works with diamagnetic anti-elements, bismuth is luckily the most diamagnetic element, of all, so good choice of fuel). Your incredibly advanced civilization undoubtedly also has incredibly advanced magnetic fields, so if we give our anti-bismuth a charge, either by adding or removing a whole bunch of positrons, you can contain it in a "tank" made of powerful magnetic fields. You'll then need to surround the whole thing with an actual, physical tank to prevent the interstellar medium, which will be hitting you at >0.9c, from slowly eroding your antimatter, but as a super-advanced civilization, I doubt building a big, absurdly durable fuel tank with a bunch of carefully placed and tuned electromagnets inside will be a problem. Additionally, since your magnetic fields are going to need to hold a huge mass of anti-bismuth against 1g of acceleration, they'll need a ton of energy input, but since your ship runs off antimatter, I doubt electricity generation is much of a problem. Note that this also means that you'll have to allocate more space for your antimatter storage than your normal fuel storage, so make note of that when drawing up designs, although how much extra room you need depends on how advanced your civilization is. You're also going to want to store both your bismuth and your anti-bismuth as liquids, to allow you to actually use them as fuel without having to somehow chip off chunks of solid antimatter. This will require keeping them nice and warm, above their melting point, so don't forget to include some heaters in your design.
2. You're not just going to produce gamma rays (but that's a good thing)
Contrary to popular belief, if you smack a chunk of matter into a chunk of antimatter, you don't just get energy. (well technically, if you smack a positron into an electron, all you get is gamma radiation, but since we're talking about anti-bismuth and bismuth here, we're going to have anti-protons and anti-neutrons involved too). You'll get some gamma radiation and a bunch of high-energy particles, some charged, and some uncharged. Unfortunately, you're probably going to have to waste the gamma rays, as we don't actually have an effective way to utilize them because as far as we know, nothing reflects gamma rays. The thing you're going to be using as thrust will have to be the charged particles (pions to be precise, not that it really matters), which will make up about two-thirds of the energy from the annihilation event, with the other one-third being those wasted gamma rays. You'll have to use a magnetic nozzle to direct them, which will probably look like a wide, thin, curved ring attached to the back of your ship with a few support struts. So that's what the bottom of your ship is going to look like, rather than a bunch of parabolic dishes.
If you handwave in a material your society has than reflects gamma radiation, feel free to build a physical rocket nozzle out of that to surround the magnetic nozzle (this would probably just appear to be a standard rocket nozzle, rather than some sort of lattice of parabolic dishes), but be aware that that's stepping pretty far outside our current understanding of physics. Everything I've laid out in my answer has been "super-advanced, but definitely possible", a gamma-ray mirror is definitely outside that realm.
So, assuming your advanced society lacks any handwavium gamma-mirror, your ship will look like kind of like a skyscraper, especially near the top. The very top part, where the crew lives, will probably be rectangular or square in shape, to give the pesky humans their nice, regular rooms, and, depending on the height of your spacecraft, may include some radiation shielding seperating it from the rest of the ship to prevent gamma rays from the drive giving everyone cancer, although the intervening mass of fuel helps with that, and as it is used up, the amount of radiation decreases as the drive power is turned down to maintain constant acceleration, so that works out nicely. The fuel tanks, below this, will probably be cylindrical, to save on tank mass and the number of electromagnets required to keep the anti-bismuth contained. These tanks will likely be stacked with the bismuth tank above the anti-bismuth tank, to simplify the already horrific engineering involved in transporting the anti-bismuth to the engine without letting it touch anything. The engine, at the bottom, will appear to be a wide, thin angled ring (or possibly several concentric ones), attached to the hull by struts. Inside this invisible magnetic nozzle, bismuth, carried from the upper tank, will annihilate with anti-bismuth from the lower tank and create a flood of gamma rays and charged pions. The pions will be funneled away from the spacecraft by the magnetic nozzle, providing thrust, and the gamma rays will spread out randomly in all directions, and hopefully not give any of your scientists cancer. There may be some visible light from the interaction site, and surfaces at the base of the ship may glow as they give off the energy they absorb from gamma radiation, but there will be no visible drive plume.
