Aiming torpedoes at different parts of ship

[Threadfin]

You don't have to switch back to auto, you can update the periscope bearing by clicking the checkmark on the datatpad while staying in full manual TDC.

So it's just a matter of setting up the TDC as the above post says, then aiming the periscope, click the checkmark to update the bearing and fire.

If using auto-targeting just don't lock the scope, simple as that.