Hi, Bones. As far as I know, there are 3 ranks for each group of seaman, petty officers, and officers.
Medals: They can improve the endurance and performance of your crew, for example faster reload times for your torpedoes, flak guns, and deck gun.
Qualifications: Giving qualifications to your petty officers can increase the efficiency of the compartment in which the officer is specialized in (gunner, flak, torpedo, etc.) Qualifications are useful, so don't count them out.
Transfer: Yes, your crew come along with you when you transfer to another U-boat or flotilla. Transfering to another flotilla can allow you to obtain a boat that isn't available in others.
There was a community manual but it's no longer hosted. Here's the link to the thread with the download link.
http://www.subsim.com/radioroom/showthread.php?t=130845
Hope this answers your questions. Good hunting.