Look at the thread stickied at the top of this forum:
Sub Skipper's Bag of Tricks-- Techniques, Tactics, Tutorials, Videos That's your best resource for learning how to play the game. The official manual is almost worthless.
This game is one of the best sims of any kind I've ever looked at. I'm another guy who knew almost nothing about submarines a few weeks ago. Just by lurking a lot and reading everything people have been writing here for years, I've learned basic competency with manual targeting and am gradually weaning myself off map contacts. I won't turn off the external views because I love looking at pretty graphics and taking screenshots, but it's easy to be disciplined enough not to use the cam to cheat. In battle I only use the external view to watch the torpedo hits (or misses) after tracking the target and setting up the shot.
There are soooo many mods for this game, for so many specific tastes, asking for general recommendations isn't going to work out so well. Just read up, see what's mentioned most frequently, and start trying them all out. You'll figure out which ones are good for you.