#1
do you usually want the Master Volume higher. or the regular volume? also on pedals do you want to lower the amp volume and make the pedal volume higher or what?
#2
You want to find a balance that sounds good to you (and preferably to whoever is listening to you). Different amps respond in different ways and the only way to find out for sure is to play with it.
ESP LTD EC-256 and a Fender Deluxe VM
#3
Check out the Ultimate Settings sticky on UG. Very helpful and detailed.