I think the first step to build anything is to imagine what size you want it to be. Generally you can just use the 2 block height of your astronaut as a good start to see what sort of scale you\'d be using, just to get a feel for how big you want your ship to be.
No matter if it\'s fighter sized, transport, or a warship, I\'d frame out the outside borders of your hull, a skeleton of sorts to start from. Basic power seems to work most efficiently to have a single or dual shaft of generators running the length of your ship, and that should be more than enough juice unless you\'ve got some massive power hungry weapon systems in mind. (and who wouldn\'t love that)
Engines are a nice look to have separately on the back of your ship, but I\'d make sure they were all connected into one engine system underneath the hull to get the most power out of the blocks you\'re putting into it.
For weapon systems or salvage, try to leave room to squeeze your astronaut into whatever space you want the output to be, since you have to get out and manually set the \"primary\" block yourself, as far as I know.
Empty space isn\'t always a bad thing, but overall, I\'d flesh out all your components and make it functional before you \"skin\" it, and make it look like the finest beast you had in mind.
-my 2 cents

Hope any of that ramble helps! Have fun!