Before I switched to GWX, I did some kind of slipshod editing of the *.cfg files in the program files/ubisoft/sh3/data folder. I think you just have to pick through the "flotilla.cfg" file for your desired flotilla. There's an entry for each flotilla that determines what u-boat you start with.
Sorry to be so vague, but I don't have the files I changed on hand for reference.
You might also check out the mod forum on this board. Good luck.