A lot of us would like some system for designing spaceships, at least in outline, for use in games, detailed fictional settings or physical or virtual 3D modeling.
The procedure I have seen most often begin by defining a hull. This gives you the main dimensions of the spacecraft, its surface area and volume capacity, perhaps along with constraints such as maximum load and drive acceleration. This is a natural approach. I used it for my battleship-era warship specification sim, SpringStyle, and it is retained by its independent offspring, SpringSharp.
But for deep space craft it is seriously misleading. Ships and aircraft, says Captain Obvious, move through a fluid medium that shapes and constrains their design. Deep space craft do not. Their overall design constraints are more architectural: supporting the craft against its own thrust, along with stresses from attitude change maneuvers, the thump of docking, thermal flexing, spin loads, and the various other kinds of abuse that spacecraft are subject to.
This is as good a time as any to point you to the Atomic Rockets pages on basic and advanced design.
I will argue that deep space craft have essentially two sections that can largely be treated separately from one another. One section is the propulsion bus - drive engine, reactor if any, solar wings or radiator fins, propellant tankage, and a keel structure to hold it all together. The other is the payload section that it pushes along from world to world.
There are both conceptual and economic reasons to treat them separately. Conceptually, because a propulsion bus might push many different payloads for different missions, such as light payloads on fast orbits versus heavy payloads on slow orbits. A little noticed but important feature of deep space craft is that you cannot overload them. They do not sink, or crash at the end of the runway, or even bottom out their suspension. They merely perform more sluggishly, with reduced acceleration and (for a given propellant supply) less delta v.
A very large station or hab might well have a modified ship drive as its main stationkeeping thruster. Or it may rely on a ship coupling to it, as the ISS is shunted by Soyuz craft docked to it.
Conceptual logic is also economic logic. The outfits that build drive buses would like to sell them to lots of different customers for a broad range of assignments.
This is not necessarily an argument for true modular construction, with drive buses hitching up to payloads on an ad hoc basis like big-rig trucks and trailers. Building things to couple and uncouple adds complexity, mass, and cost - plug connectors, docking collars, and so forth. Moreover, drive buses intended for manned ships need to be human-rated, not just with higher safety factors but provision for supplying housekeeping power to the hab, etc. But these things, along with differing sizes or number of propellant tanks, and so forth, can all be minor variations in a drive bus design family.
The payload we are most interested in is, naturally, us. The main habitat section of a deep space ship closely resembles a space station. It is likely that habs intended for prolonged missions will be spun, for health, efficiency, and all round convenience. (Flush!) The design of a spin hab is dominated by the spin structure and - unless you spin the entire ship - the coupling between the spin and nonspin sections.
Because ships' spin habs have the features of stations they may be used as stations, and again we can imagine design families, with some variants intended for ships and others as orbital platforms having only stationkeeping propulsion. Habs are the one major part of a deep space ship that correspond fairly well to our concept of a hull. Spin habs are entirely different in shape, but the shape is constrained; once you build it you can't easily modify it, beyond adding another complete spin section.
Pause to question another familiar convention here. Since at least Heinlein days spinning ships have typically been given a control room located on the spin axis, and perhaps nonspinning, where the astrogators can use their instruments unhampered. But isn't this equivalent to the circular astrogation slide rule? The navigators will do their normal work on monitors. In the inevitable space emergency there will no doubt be coelostats available, or other workarounds. But there's no reason not to locate the ship's main operating control room in the spin section, closer to the people who work there.
Though I'd be happy to be persuaded otherwise. I have always liked Heinlein's penthouse style control rooms at the forward/top end of the ship (plus the fact that he never called it a bridge). If Hollywood came calling I'd bend realism here in a nanosecond, not least because a 'top' control station is visually easy to understand, a sort of Aha! moment for viewers. But I suspect it is a minor cheat.
For those with bank cards at the ready, buying a deep space ship might be not unlike buying a computer. If your mission needs are fairly standard, you check off options on a menu. Those with more specialized requirements can select major components - perhaps a drive bus from one manufacturer, a main crew hab from another, along with custom payload sections, service bays, and so forth, assembled to your specifications.
In fact, both technology and probable historical development suggest that fabrication and overall assembly will be two distinct phases, carried on in different places, quite unlike either shipyard or aircraft assembly practice. In the early days, large deep space craft will be built the way the ISS was, assembled on orbit out of modules built on Earth and launched as payloads. In time fabrication may move to the Moon, or wherever else, but final assembly (at least of larger craft) will continue to be done at orbital facilities. I call them cageworks, on the assumption that a cage or cradle structure provides handy anchoring points for equipment.
For game or sim purposes, my advice would be to treat drive buses and hab sections as the primary building blocks for ships, whether these components are permanently attached to each other or simply coupled together. Both approaches might be in use.
A couple of provisos. All of the above applies mainly to deep space craft, especially with high specific impulse drives. Ships for landing on airless planets have some similar features. Ships that use rapid aerobraking, however, are aerospace craft and broadly resemble airplanes, even if they never land or even go below orbital speed.
And I have said nothing of warcraft. Kinetics are essentially just another payload. Lasers, and other energy weapons such as coilguns, probably draw power from the drive reactor, calling for some modifications in the drive bus. These things don't much affect the overall configuration. Armor protection would, but discussions here have left me doubtful of its value against either lasers or kinetics. Laser stars and other major warcraft may not be dramatically different in appearance from civil craft of similar size.