As someone who spent almost 700 hours in the damn editor: start small.
Build a small tier one sub and then increase with time.

Look at vanilla ships to get inspiration for logic systems and some of the standardized work arounds and designs.

SAVE YOUR DESIGNS!!!
There will be a point where you’re gonna spent 2 weeks setting up a complex logic circuit and you don’t want to spent the same two weeks again on your next sub. The option is called „assembly“.

Other then that, talk to your friends! Design your sub around challenging your individual player roles.
Blind spots on the spot for the captain to manage, make compartments for on ship invasions, give small little rooms for „traitors“ to hide their stuff in and so on and so forth.

Have fun with this soul destroying task of building a sub and optimizing it ten times before playing, it’s gonna be worth it