That is a pretty crazy setup. It seems a little backward though, but if anything the rotating pipes on the top are really cool and you should keep it just because of that. The pot scrubbers would do best in the towers, or at least elevated off of the bottom of the sump portion so that they are not submerged.
I think that the best way to go from there would be like this... Leave the rolls were they are, maybe cut them in half, so that they are 6 in thick. Then fill the bottom half of the tower with the pot scrubbers. Get a plastic lite cover or egg crate, something that will hold the rest of the pot scrubbers and hold them out of the water. That should work pretty well, and if you needed additional filtration you could add a FBF. Then you should be pretty well set. but you might want to have some sort of prefilter before the pipes unless they come off and clean easily.