Most of the time I aim for two biggest ships, firing 2 torpedoes at each ship. My optimal distance is 2-4 km. I try to pick ships in the same or adjacent columns, to avoid shooting with large gyro angle (larger distance helps). When attacking submerged, I don't bother to move or change my position. I just wait for the selected ships to come in front of my tubes.
When attacking ships at different distances, you have to carefully time the second shot in order to have all impact at the same time.