I don't spend torpedoes unless I absolutely have to. Well placed shots on keel with the deckgun can sink Coastal merchants and Armed Trawlers in less than 5 shots.
Save on Flak ammo, especially after 1943. You'll need it.. Manually gun flak if possible.
ALWAYS operate the hydraphones yourself, don't trust your SO unless you're preoccupied. I'm convinced my Sonar Operator is either a tommy spy or he left his hearing aid back at the sub pen.
Try to get abeam from your targets at a perfect 90% angle, even if using magnetics. I tend to stay away from magnetics though, especially early on in the war.