I just started playing, and one of the mods I starting using is called something to the effect of 'Decks Awash & Fuel Economy' mod. It sets the periscope depth of Type IIs to where the conning tower stays submerged in rough weather, sets the 'Ahead One Third' command to the subs optimal fuel economy speed, and allows you to run decks awash by hitting the 'snorkel depth' key.
http://www.subsim.com/radioroom/down...o=file&id=1183