Check this link for some great tutorial videos!
http://www.subsim.com/radioroom/showthread.php?t=146795
MOD selection is a very individual thing, read all the posts about each one and see what toots your horn.
As for 100% realism go for it but I personally prefer to learn one major part of captaining a boat at a time. While learning manual targetting I don't want to have to worry about my fuel or batteries running our or moving my crew around during different events. Also while learning manual targeting it doesn't hurt to have "realistic load times" uncheck so you get reloaded faster, just gives you more time to learn to hit something.