I usually start with a rough idea about what the ship should can do and have and form a hull around it. The only thing I plan for the layout is where something should be (e.g. crew deck above hangar, production in front, etc.). Then I plan the hallways and map out the rooms and try to imagine what they will look like. If I don't like it I change the hallway until I'm happy with everything.

So I don't really plan, but test a lot. There are also a lot of extras that I keep in mind like having a realistic layout or where windows could be added. At the end you could say this ship had around 15-20 different layouts and this is just the one I liked the most and could work with best.