Welcome aboard!
Firstly, since you are calling the ships a "C2", it seems you are running stock SH3. In stock SH3, you can, believe it or not, "one-shot" C2 cargo ships. The trick is to aim your periscope directly under the funnel. This is assuming you are not doing manual targetting, of course.
Second, take my advise - avoid magnetic pistols. I've been playing this game for a few months now, and gave up on them long ago. In fact, just last night I had my first and only magnetic detonation - I was in a tight spot with a destroyer and, having heard others do it here, tried for a "head on" shot with a magnetic pistol (impact pistols are no good at angles - the torps skip off of the ship's hull). The torpedo went off and did sink the destroyer, but nonetheless, I never use them. Stick with impact pistols.
Finding ships should not be very hard, except in bad weather when your lookouts can't see them. When you get a map update that shows you a contact, you will also see a "tail" coming off of it. This tells you the direction the contact is going. Use the ruler tool and draw a line from the contact out in front of it a ways, parallel to the contact's tail. This gives you an approximation to the ship's course, unless it changes course. Then just use your waypoints to plot a good end-around intercept, like a letter "J". The idea is to fly along at flank speed until you can get out in front of it, then submerge and slowly creep up to interception. On your creep leg you should pick up a sonar contact for your quarry, unless, again, it changed course.
Good luck!
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