I have burrowers and clip the fleece down by cutting out a small area on the coroplast and pulling the fleece through. It keeps them from going under it and makes cage cleaning very easy.
For underneath, I use a mattress pad and two layers of towels under the fleece and then a kitchen area (I made a coroplast box) and I put Yesterday's News with a layer of Carefresh over it. This has been my best solution for odor control and ease. I would personally suggest making your cage a grid length longer and adding a kitchen area instead of an upper level. I removed my upper level after a week or two because it made it so much harder to clean the cage. But again, this is all just personal preference. I lot of people do have upper levels so they must work out fine for them
