No worries.
Manual targetting is something that we do need to explain better for GWX in the manual with the update that is in the works.
If you do install GWX, the manual will explain all significant changes. You can find the GWX manual ('das Buch') in your SilentHunterIII/documentation folder.
Concerning player game mechanics / player control of the game itself. We made great efforts to make sure that it remained/remains intuitive for those making the jump from stock SH3.
Events that happen external to the U-boat that do not require input from the player... Well, that is naturally an entirely different animal.
BwaHAHAHAHAHAAAaaa!!!! 
At any rate... a player only has to use complicated math if he chooses to.