Generally, a close stance is used for ME box squats (according to the general Westside template). There's no reason you can't use both wide and close stances if you want to. The reason for the close stance, however, is to put more repsonsibility on your lower back during the lift.
Yes always try and sit back. If you use a closer stance, though, it'll be harder to sit back on the box because of the different leverages you have created.
By pushing your knees out, you recruit different muscles. By keeping them together, you put more stress on the quads. Again, that seems to be up to you. Close/wide stance and knees out/in just creates more ME box squat variations.
The weight is heavier on ME box squats.
%s don't really matter. ME box squats are just another lift to test your strength and make you stronger. And they'll do that.
Just use a closer stance on M.E. You should still try to sit back but remember that if you are using a close stance you may not be able to sit back as far as when you do D.E. squats. Dont worry about percentages, like most other things, this varies from person to person. But if your box squat goes up, I bet your comp. squat will go up too. Remeber to still release the hips when you hit the box and then explode up. Some people have a tendency to want to rush it and bounce when the weight gets heavy.