A sump is an area to place equipment like heaters, ATO, skimmers, and other equipment. The rim of a tank can fill up quickly, just like your rim. People do not like looking at those equipment, so they get sumps. Sumps can be setup in many ways. There are pros and cons to everything, so it takes a lot of time researching to figure out how to eliminate as many cons as possible from a sump.
My tunze is hanging over my tank rim on my 46g. I have the normal size one, not the nano version. You might want to contact tunze via call or email to see if you can place a nano in fluval.
Best way to keep your bottom clean is to take them out manually as you are doing now. Maybe use a baster to suck out waste intermittently in between water change.