Not sure what others do but when I clean out my filters, I physically remove the entire filter from the aquarium, take it over to a utlity tub and clean out the filter media in the tub, that way all the "crap" goes down the drain and not into the aquarium. Please note: I do not scrub the inside of the filter as you want to keep that slim intact as it is all the benificial bacteria...
Good Luck !