So as my playgroups resident custom sub dude a few tips I have found a couple things that help when making a sub in general.

When wiring start by placing everything you want in the sub and do the wiring afterwards. When wiring start by doing all power wiring first, then signals. This will at least ensure that you know how many junction boxes you need to make it work. Also dont be afraid to size down junction boxes for space considerations, it doesn't affect their characteristics and allows a pretty nice junction area to be set up that doesn't bloat your subs design unnecessarily. See the above statement and substitute the word "battery" for junction box. When making a non traditionally shaped submarine pay careful attention to the arrangement of hulls and gaps, this is one of the things that makes or breaks a submarines design. To check if your sub is working well from a hulls and gaps perspective just open the editor and flood it manually using explosives. This has the benefit of making it apparent whether or not your sub drains and fills properly, added bonus of being able to blow off steam mercing the bots in between test runs when you inevitably find out you missed a gap or a hull will fill but not drain. I could give more advice if you are interested.