The usual way to scratchbuild any spaceship in a larger scale is to build an inner structure of decks and bulkheads. You could do the same, but leave off the outer planking, which would normally be glued on, but in this case could be fixed with magnets and steel sheet (if you add the magnets to the central structure, steel sheet on the outer skin saves you the expense of extra magnets). For a spaceship, it might make sense to have the top outer skin (or "roof") lift off for the upper deck, and the sides for the lower decks.
The key point is "breaking down" the overall shape of the space ship into geometric shapes, like cubes, pyramids, cylinders etc.
Remember to add doors to the bulkheads before you glue them in (obvious, I know, but mistakes like those happen).
You could then detail the inner walls (although for some hard-to-reach areas, it might be sensible to do it in advance). I would suggest leaving interior furnishings (like chairs, cryochambers, and stuff like that) off, which makes them easier to paint, and you can position them differently if you feel like it.