Well in terms of the locked on feature you probably know that that is a total fabrication, an intellectual conceit in favour of the solo play aspect of the sim. Being married to it as a primary function though alters your relative flexibility when firing at more than just the centre of the target.
The dial which Avatar is referring to is the Angle on Bow setting. This is edited in both the (F6) TDC screen as well as the note pad. Off the top of my head I can't be sure which way to tweak the settings to get a different result but if you experimented then you could get it right I suppose.
The fact is that if you want to maintain your target lock while still selecting which part of the target to aim for then you will always have a bit more work to do than if you did it the traditional way. The purpose of the crosshairs in the scope and for the TDC computer to be tied to the rotation angle of the periscope is so that you may target particular parts of the the ship. Attempting the same result while using a different method will always be difficult since you are not using the equipment as intended.
My advice is to just unlock your crosshairs and aim that way for best results. Your way involves a bit of guesswork. But thats cool. Since the WO solution is always correct, tweaking it will work fine.
Good luck and let us know about how it goes.
