I've only ever played with the WoS megamod, so I can't comment on what it does without it. Also I don't know how to change u-boats; I assumed that was not possible.
Here is what it looks like when I'm in my loadout screen in base:
http://i.imgur.com/D3UR1g9.png
And here is what it looks like when I start a new patrol:
http://i.imgur.com/Gb7xoJ5.png
Now I've gone a couple of months now (October-Dec 1940) without being able to select a mission. Maybe if you start a patrol without selecting a mission this is what you get?
Steve