My 2nd Patrol and Advice for promotions and upgrades..

[enaceo]

I use NYGM mod ,so managing the crew is a bit harder and efficency is more realistic.So,while using NYGM i usually take a torpedoman officer ,and then i give the gunner and flack speciality to my watchman since i usually start my career in the early years when deck-gunning is used more.
When i was playing stock SH3 i also took a machinist or torpedoman officer ,depending mostly on what type of ship i was on.
I'm not so sure what the sonar/radio skill actually does,but it probably increases the efficency of your radar/sonar/gramophone or whatever you use as a sensor.
Yes,you do keep your crew if you get a new sub/or get transfered,and i'm not sure you can actually transfer somewhere and get the IX right away.You could do that using SH3 cmdr but that would be kinda cheating.