Hey Saint. To answer your third question first. Run wire to all the places you have listed. If you run them to both locations you suggest for your 5.1, you'll be set for 7.1. This, in part, should help with decision making for question 1. I'm the type that likes testing things. So I'd suggest to run wires to both locations, and go from there and see what sounds better to you by having a friend (or preferably two) hold the speakers in the locations (the sides one time, then the back loaction another) they'd be hung and go by what your ears tell you.
To answer question 2. Do as much as you want. But, unless you find people peaking back behind your speakers or it's very viewable from everywhere, I wouldn't worry too much about running the speaker wire into the wall for the fronts. I'm sure they'll be to captivated by the wonderful sound to care.
Good luck and have fun!
