I think that the way you're thinking of doing it would be fine, and pretty smart! When I was making liners I originally tried something like this - a piece of fleece folded over, with a layer of cotton batting in between, then sewed on all the sides. However, it was a terrible mistake - on the first wash the cotton part got ripped from the thread and all twisted up between the fleece, plus it got all wet and started falling apart. Obviously the person at the fabric store sold me some cotton that was not washing machine safe, but it was enough to not try again. I ended up taking out the stitches on one side of the liner, removing the cotton, and sewing them up again. (Caveat: I sewed all of this by hand, so my poor sewing skills probably didn't help matters.)
That said, the two layers of fleece works great! Totally absorbent and easy. I put two paper towels under Liam's wheel as well and change those out every morning. He's pretty good about pottying only there (he never took to a litter box but for some reason paper towels are okay
) but I do a spot check and clean in the morning as well.
Anyway, main point: I think your idea would be great, if you want to put in the time and energy. But, if you don't, plain fleece on its own works well too.