Welcome.
Yes the manual is nearly useless as a game aid. Check the Tips & Tricks thread near the top of this section. You'll find a lot of useful information posted there.
I just wanted to add that, whatever you do,
don't click on those shortcut buttons (ie. surface attack, etc.) that you see in the crew management screen. If you do the game will very likely ctd (crash to desktop). This is a well known bug that exists in both stock & modded versions of the game. Unfortunately nobody has been able to fix it so move your crew around manually to avoid this problem.
Like Sharkbit said, play around with stock until you're used to it then prepare to be blown away by GWX & SH3 Commander.