1) Yes you can
2) You can use it whenever you want provided your surfaced, question is how useful it is in bad weather conditions
3) Press F6 for the attack map, if you have a solution a predicted torpedo path is displayed.
4) You can move it around with mouse and arrow keys
5) No, generally; surfaced: if you can see the enemy they can see you. Submerged: Didn't you pay attention while attending subschool?

There are some great guides on both passive and active sonar posted somewhere.
Search the "Subskipper bag of tricks" tread. edit:
http://www.ducimus.net/sh415/ai.htm
6) Yes there is, the recognition manual has it al.
7) In the damage screen top left displays hull damage in %.
8) No that is not normal, guess something went wrong with your realism settings.
9) Only when your sub has been damaged.
10) No, just drag and drop.
11) There should be an enemy target around
Tried to answer your questions at my best knowledge, but i'm not the most experienced skipper around..