The point of the paper is to NOT have any loose substrate in there during the healing process. You don't want the aspen holding onto excess moisture or bacteria, or sticking to the wound. With paper, you can tell instantly if its wet/dirty and clean it right away. So...the paper does not go on top of the aspen...nor the other way around. Just paper.
Newspaper is simpler to work with, I think...you can fold a big sheet and it will generally stay in place, although some snakes seem to enjoy shifting it around and even hiding beneath it. (Same with paper towels) The point of having anything at all in there is so that you have something to absorb waste when the snake pees or poops. Just a couple of layers should be fine. BUT...this is why I stress having some sort of control over your heat...because you can't control how much contact your snake my have with the surface just above the heating element. Even with loose substrate like aspen, they can and will burrow down beneath it and lay on the surface of the glass.