[postalbyke]

I play almost exclusively with type II. I recommend having four machinist chiefs (two on-watch, two in quarters), one watchman chief (in the bridge), one torpedo chief (in the engine room), one flak chief (in the aft quarters with the machinists), two radio chiefs (one in sonar, one in forward quarters), then flesh out the watch sections with seamen (should have a full loadout of seamen and chiefs) for the officers, i recommend weapons officer to be torpedo qualified, kept in aft quarters until needed for attack or crew change for fatigue, and watch officer to be flak qualified.
to refresh the crew, i go to 25m, swap everyone out, time compress 32x until everyone is recharged at least 3/4, then i pop back up and carry on.

edit: I don't worry about repair specialties yet because i've never been successfully attacked! dive early, dive often.