Quick colour key, here's what I got so far. Will finalise a colour key in a bit:
White: Walkway. (Don't ask how things connect together just yet)
Dark Red: Weapons
Light Red: Different Weapons
Green: Residential (In Deck 2, the bits off to the side are the Crew Quarters, the bit in the middle is the mess hall, the two triangles are kitchen and storage)
Yellow: Airlock (notice how close they are to science)
Cyan: Science
Blue: Sensors
Grass Green: Bridge
Purple: Computer systems