Well, the best place to learn the game is at the Commanders Academy and Dive Center!
I'd try this thread.
http://www.orionwarrior.com/forum/showthread.php?t=40
There are also many very good guides available for download at the CADC, as well as Bill Nichols
www.subguru.com , which is the best place for user created missions!
My personal advice is to start with the Kilo, and once you get a hand on all the stations and how the Nav Map and battlespace work, you can either move on to the 688i if you want another sub, or try your hand at the MH-60.
Welcome aboard!
Cheers,
David