Altough I have no evidence to back it up, I would think a lot more snakes have died from impaction due to aspen ingestion as compared to paper towels. I've used every substrate I can think of and PT are definitely my favorite. Never any issues, easy to clean and cheap.

To answer your questions, I overlap my paper towels in the center but basically one layer around the outer edges of the tubs. And yes, clean the whole thing whenever they make a mess. I'll also replace it if they make a mess with their water bowls or bunch up the paper towels on one side of the tub. It's super cheap so why not?