Do you use SHCommander? It lets you do almost unlimited tweaking of your crew. I would say without a doubt that Commander is the reason I still come back to SH3 again and again and again.
This is the officer breakdown I tend to use-
ENGINEER- Usually most senior officer(but not always) Qual- Helmsman, Engineer, Damage control
1ST WATCH OFFICER- Considered my XO. Qual- Watch, Torpedo, Damage control
2ND WATCH OFFICER- Qual- Watch, Gunnery, AA
3RD WATCH OFFICER- Qual- Watch, Helmsman
I try to keep the Engineer with the boat as long as possible unless he is killed, transferred or fails to return from leave.
The watch officers I expect to be transferred out eventually as they are needed on other boats or to assume their own command(my random choice or Commander's).