Have you roughed out any other areas yet or do you want to get the engineering room perfect before moving on? I do my modeling in the physical world as opposed to the virtual one. Part of my methodology is to plan out the entire build in rough form so I can get a handle on the scope of the project, then start layering in the details and fine tuning it.
Not really, when I started I was only planning to do engineering. Then I started fleshing out other parts of the ship and its kind of balooned from there. There's no master plan or goal really, I'm just doing it for fun but its starting to really take off now.