I have always assumed that being a commander in a war is less a matter of personal preferences (how to do things) or outstanding physical properties (eyesight, strength,...) but of what we'd call "management skills" i.e. good leadership, sound judgement and taking the right decisions - decisions that would then be executed through well established routines with roles and responsibilities clearly laid out.
The "Submarine Torpedo Fire Control Manual" devoted
Chapter 4 to a description of The-Torpedo Fire Control Party and
Chapter 5 to the Duties of the Fire Control Party.
Given that the manual was issued in 1950 and by the U.S. Navy (and not 1939 by the Kriegsmarine) there might be quite a few differences, but still one gets the picture of who does what ...
Of course, a good commander always knows what is going on and performs reasonable checks. Doing a task himself if there was an assigned officer or crew should have been a very rare exception ... (or an insult to the officer/crew)
My personal guess is that the most important thing the commanding officer would have to do himself would be to verify the validity (flag, ship type) of the target, select the attack strategy (torpedo/gun, submerged/surfaced, course, attack position), and give the command to fire. (now that would not make a very exciting "video game" would it? that's why in SH3 we get to do all the tasks ourselves, if we so desire
)
regards
Helmut