I agree there are certain limitations to the map and tools. When you see the pro's do it they do make it look easy. Getting the speed correct is paramount and the most difficult part for me. With experience you can get approximations which you can confirm with a good plot.
I do not have an answer except to suggest, pausing the game and working a plot on paper or electronically on MoBo, I have used both with success.
I also went to a "real" chronometer, got one on ebay used. Very nice and much better to implement than the ingame chrono.
You will have to experiment and come up with your own methods, over time it does get more intuitive.
My favorite is a hydrophone only attack, send parameters to the TDC, plotting course and speed, setting up the boat and then confirming with a 7 second periscope peek and back down. That is very rewarding especially when you get hits. But then again there is that pesky torpedo problem to contend with.....
Happy Hunting!