[sublynx]

As Vonharris said. Tick realistic crew transfers and you get your crewmen rotated. Officers can be managed if you hit "click for available options" in SH3Commander's main page. Then click "manage your crew". You get a screen for each of your crewmen and officers. If the officer is considered experienced enough to be promoted out of your boat, it will say so in "suggestions". Dismiss the officer and get a green officer the next time you visit the barracks.

If you tick "simulate realistic career length" in SH3Commander's options, the program will even retire your captain, if he gets experienced enough. The most successful U-boat commanders became some kind of heroes in the eyes of the German public and after losing Prien, Kretschmer and Schepke in a few days, the Kriegsmarine started rotating the commanders out of harm's way. Losing the popular commanders was considered bad for morale.