Check out this thread>>>
http://www.subsim.com/radioroom/showthread.php?t=159617
it explains how to change the schnorkel depth setting (available but unused for Fleet Boats) to decks awash, and how to activate the command through the ";" key.
I found it pretty easy to make the edits. You have to do it for every sub type, and you'll have to experiment to find the best depth setting for each sub.
g'luck