Unless you have selected manual targetting, the torpedo (weapons) officer will have entered the peoper speed, course and distance into the torpedo computer )TDC). All you need to do is aim at the part of the ship you want to hit.
If you press L the periscope will lock on the center of the ship. If you want to hit another seccion, press L again and aim the cross hair at the spot you want the torpedo to go.
Looking forward to seeing you operational, soon