I picked up Dangerous Waters pretty fast. Then again, I had played Sub Command and before that, 688i Hunterkiller. 688i had a FANTASTIC tutorial in it's manual. Once I had mastered that, it was just a hop skip and a jump to most other platforms.
There are a LOT of Dangerous Waters guides here that might help:
http://www.subguru.com/downloads.html
You definitely came to the right place to ask your questions.
Like the above post states, if you could tell us what parts you don't understand, we could help more.
Another way of doing things is to meet up with one of us in a multiplayer scenario (maybe start out with one that has no enemy vessels) and work on tracking single or multiple targets, then work on torpedoing one, and work your way up.
You know, A Dangerous Waters live tutor program would definitely be a benefit to the community.