I set up my manual solution with the target locked, just before Im ready to fire I "unlock" the target and then hit the "check" box to accept the solution and then wait for the part of the ship I want to hit to pass through the cross-hairs...the fire. If I want to aim for the forward portion of the ship I "unlock" the target, move the cross-hairs forward of my forward aiming point, hit the "check" box to accept the solution and then fire when the point I want to hit passes through the cross-hairs.
I always aim for the smoke stacks first, its almost always a sweet spot, it will typically bring your target to a screeching halt, or slow it dramatically. My secondary target is the last 1/3 of the ship in hopes of blowing out the screws if the smokestack/boiler room hasnt crippled her already, and then my last priority is the first 1/3 of the ship. There is typically nothing up front but compartments to flood to help bring her down faster. The key is destroying the ship means of propulsion, plus the added benefit of the engine rooms potential to cause catastrophic secondary explosions/damage. If the 1-2 hits to the back dont bring her to a stop, or take her down quickly, the added weight in the front from the 2nd or 3rd torpedo's flooding of the nose will make the ship drive itself under.
