After you've gone through and researched what you need, you'll want to make sure you have the parts. When Kelso (and he could tell you better) is building a huge micro ship the parts number is just mind boggling. If you want to go minifig scale... wow.
I would also strongly suggest using something like LDD, if not just drawing things out on draft paper (or something with lines). When you're talking minifig scale, you're going to want to know what kind of space you have for interiors and how you need things arrainged so the figs actually have room inside.