Personally, I use Commander to hand out qualifications to all my crewmembers (Enlisted included, though I dunno if that has any effect at all), and hand out a U-boat badge to anyone who still doesn't have one after their 2nd patrol.
I also turn on SH3 Commander's transfer setting, and when I get a new crewmember I qualify him after the next patrol (Since commander closes after you get the transfer popup). I usually lose them by the next few patrols or so anyways, but hey, at least someone else out there has a qualified sailor now.
