First, install SH3 Commander. It will do so much for your game you'll wonder how you ever lived without it.
Second, open SH3/Cfg/U-boat availability. There you will find the start dates for all the boat types. Simply change the dates to what you want. The IX-B in 1939 is historical; the IX-D2 is not. If history isn't what you're after, that's cool too.
If you get that far and still need help, just ask.