WELCOME ABOARD!
Mr. "I don't know anything but I'm very patient" (that's me) is here to help. I understand that even the simplest things can be confusing sometimes, mainly because I'm simple myself.
I would invite you to PM me with any problems, but I'd also like to keep everything out in the open so anyone else who happens along can see each step.
STEP 1: Navigation. First rule of learning: In the SH3 game folder are two files labeled SH3_QRC_PG1 and SH3_QRC_PG2.
PG1 shows you all the in-game hotkeys, which keys to push to make things happen. This will become second nature in time, but when you are playing these are also available by pressing the 'F1' key.
PG2 shows the keyboard layout, including what each key combination does.
There is also a manual in there. It is pretty much useless, but it doesn't hurt to give it a look anyway, since any question you have will be answered here.
When in the Navigation tutorial, the radio messages will tell you to click on certain functions, and will also tell you which hotkeys duplicate those functions. At the bottom right of the screen are three dials. One is the depth guage. You click on it to set your depth when the message says "Go to 25 meters". When it says "Go to periscope depth", just press the 'P' key. Another guage is the engine telegraph. It is the one that is divided into sections with funny names like "Kleine Fahrt". You don't have to memorize the names, just note that there are five of them forward and four reverse, and they translate as "Ahead Slow", "Ahead 1/3", "Ahead Standard", "Ahead Full" and "Ahead Flank". You can click on them, or press keys 1, 2, 3, 4 and 5.
That's pretty much all you need to know to earn an "Excellent" in the Navigation Class. Practice that one and ask anything you don't understand, and then we'll move on to the next one.