My balls are placed in a plastic box that hangs on the back of my tank. There's a rectangular collection cup with spill-over, being "sucked" in by a 1.5" tube, water first goes through debri filter, then over through a microfilter, oxygenator/skimmer device (basically a highpowered air pump that pushes sludge into a collection cup), then the water pours over this plastic piece that drips all over the balls. If it isn't adjusted right, the return feed can dry up killing my pump... or if I'm adding water, it can flood the bioball bin... which I guess basically just flushes everything.
I guess that's where I get my .20ppm nitrate bumps
By the way.. 6 months and no water changes. I only add about 5-10ga every 2-3 weeks due to evaporation (and random leaks *cough*).
So basically, if you dont have enough filtration before your balls, you might have to clean them.
I, personally, have never cleaned my balls. 8O