As I'm goin' down said not once but twice,
the manual is junk.
This forum is the best manual around so just ask and you shall receive.
Just play around with the orders bar(HUD) and you will soon see what everything does. As you add mods things there will change some but mostly it is enplaned in the "readme's"
Looking at your join date I suspect you have a good deal of experience.
The "bag of Tricks" thread is loaded with stuff and also the mods thread.
Here
http://www.subsim.com/radioroom/showthread.php?t=146795
And Mods here
http://www.subsim.com/radioroom/showthread.php?t=155786
All the big supermods are very good and stable so you can have your pick without worrying about them running right.
There are two big differences between a U Boat and a Fleetboat.
First is the Fleetboat TDC and Position Keeper. Much different than you have used. There are a number of tutorials on it's use.
Second is that you get to live past May 43 and win the war.
Welcome to the Pacific
Magic