I mix and match my crew management between game and commander. I like to start a career with a SH3C generated crew and stick with it, I enjoy turning these green sailors into full on officers so I use realistic crew transfers (which can really upset the equilibrium sometimes but sometimes works out well), realistic career length so I tend to stick with the uboat more than the crew and start a new career commanding the same boat and crew through SH3C, I also try to stick to the game generated promotions but rewards are awarded on individual merit and depends on the level of the patrol's success. Normally I have enough medals in game to dish out (invariably too many) but I can always supplement with SH3C if needed.
Qualifications are given out to officers and petty officers normally through SH3C and I've set a minimum of 2 patrols for the crewman to become qualified in each compartment. I also use the little known feature of the game that Commander doesn't allow, promoting between classes. I promote my sailors up through the ranks then to petty officers, then to officers. With the random transfers active I can watch a basic sailor progress through the ranks, through multiple Kaleuns and a number of different U-Boat types until he makes Chief Engineer and eventually gets transferred off to his own U-boat.
That is of course, if he and his crew survive long enough, which more often than not, they don't.
Oh and I use the no fatigue option, so the crew members can easily be organised by rank with the sailors normally in the forward quarters and the petty officers in the rear. Torpedo petty officers stay in the torpedo rooms at all times and I move the sailors in when reloading or firing is needed, unless I have no reserves left and it's just the eels in the tubes, in which case the petty officers have it covered. All new sailors to the uboat start their career in the engine room and work their way to torpedo crew, then to the control room, then watch crew, and finally the highest ranked are part of the damage control team (use LRT), until there's a petty officer vacancy.
Complicated, but works well and keeps to a realistic pattern I think.
Damo.