I was thinking of having a superstructure, and then different modules on the superstructure, and then more modules, but shaped similarly to the ship/structure, and then the hull/armor and then it's done. That is what I was thinking, are you saying that that is hard to do because of the programming of the engine?
Its just that currently the models are all in big completed pieces, and you can't just start with one part of the ship then have the others appear because they aren't designed to be taken apart like that. Even if you set it up like you'd have to make a separate model for each little component, which will substantially increase the number of meshes Sins loads. Now you could mess with the filters to get it to look a bit different, but currently you'll never be able to say "First build the bridge, then this turret, then attack this engine" etc.