First of all plz don't read the whole GWX manual, just concentrate on playing the game I would say. I would suggest referring to the table of contents when you want to know something. The manual targetting chapter could be helpfull tho. You could check this out aswell for more:
http://www.subsim.com/radioroom/showthread.php?t=146795
SH3cmdr is a must have, kind of hard to explain why but you'll see it for yourself when your using it.
Once you got both of those mods installed, I would say play a couple of patrols than come back for more. Kind of what I'm doing at the moment, because I've reinstalled SH3 a couple days ago.