My build here has 4 floors, each consisting of a different thing. I'm not that good at screenshots, by the way.
Bottom Floor: Contains controls for the ship, most are just props, but the thruster controls turn the thrusters at the bottom on and off.
2nd Floor: The next floor is spawn room, and I'm thinking of adding an armory. Pretty much.
Hanger: The hanger is... well.... the hanger. I set up emitters to make it look like it has a forcefield, and at the back a set up a small jail.
Top Floor: The top floor is open. This is where I set up my turrets, and where I made a secret room where the self destruct controls are. And when you use 'em, it self destructs. Duh.
(I can upload save file if needed, I'm leaving some screenshots out 'cause the god d*mn forums won't let me post more than 4 picts)