Just stir it up once in awhile and let nature take it's course. I have 2 current systems right now, and in the reef, the crud just sits there and gets reused and reused (there's an amazing collection of limpets, snails, calcerous tube worms, sponges, copepods, crustaceans, worms, and who knows what else in there). On the other system, I have my skimmer in the sump, and that seems to take care of any stray crud on the bottom (along with the aforementioned sump residents). Or, just suck it out. Even if the sump's on the floor, all you need to do is get a small diameter tube (use bigger than an airline so the shrimp don't clog it), stick it in, suck on it to start the siphon (don't drink the stuff, it's pretty disgusting and I always wondered how many sump creatures were crawling around in my intestines!), and suck out the crud. If you attach the hose to a small diameter piece of pipe, you'll be able to guide it around, and the amount of water you're siphoning off will allow you to maintain the siphon without having to stop it for your sump to refill (although you'll need a pretty wide receptacle for the siphoned off stuff or you'll run out of room and siphon it back in).