To add to what Railgun said, watch that you don't "refit" more than once as per Trevally's instructions. I believe this would include refits at sea from the supply cows later on in the game. Refitting too many times apparently adds to the potential for save game corruption. Remember, Allies aren't your worst enemy - CTDs are!!
I haven't done it in a while, but I think you can dock at the bunker, manualy restock your torps with the supply guy, then head out again without it affecting mission status. Don't quote me on that though, since I'm not 100% at the moment.
If you're playing with icons on, pay attention to sightings where a red icon is placed on your map. Draw a line through it if it runs through the ECW area. In time, you'll find regular shipping lanes through your own experience and you'll know where to hunt.
Do a hydrophone check every two hours. Something should come up.
And yes, use your deck gun if it's a loner. Early war, ships usually aren't armed, but later on, they are, so it will be more difficult to attack them like that without them returning the favour.
gute Jagd! ..
EDIT:
When you click on the ECW patrol icon, you see a red line marking the designated area. You don't have to only hunt between that line and the coast. You can also hunt the other way out to sea for at least 60-75 kms, maybe even more. Sunk targets will apply to your tonnage numbers.