First I started by giving the coop a through cleaning. Scrape clean, let dry, then sweep to get any remaining dirt up. Lay vinyl remnants on the floor right under the roosts. You can tack down the corners if they start to curl. Then simply cover with the bedding of your choice and your done!
I've found a plastic hay rake slides right along the vinyl when cleaning up and makes it easy to remove the messiest part of the bedding without disturbing the rest. Why vinyl remnants? Well for one they're cheaper then stall mats or custom cut rubber flooring. Sometimes they're even free. They're easy to cut with a good pair of scissors or utility knife (ever try to cut rubber mats? ugh!) and they clean up easy. You can find them at any home improvement store....or Craigslist. Floors in the smallest coops can be covered completely if you'd like. Lastly, if you feel like spending a few $$ you can get vinyl flooring in almost any pattern or color you want! I think I'll get something in blue for the grow out pen!