Currently (it's not my tank, but my parents, although I probably "mess" with it the most), I have a Whisper 30-60, which has two compartments and each compartment holds a floss-bag and a black sponge. When the floss bag gets too dirty, I take it over to the sink and thouroughly rinse it out so that it's white again and not dirty brown. The reason behind only doing one of them instead of both of them is that I don't destroy all my beneficial bacteria.
I did an experiment one day and rinsed out all of the filter media, and nothing bad happened (tested the water parameters after a while). I'm guessing the bacteria in other places in my tank, such as in the substrate and decorations quickly re-colonized the filter media. Take of it what you will, but to be safe, don't clean or change out all your filter media at one time. I find cleaning my filter media under the sink, rather than in spent tank water (so your bacteria doesn't die), is a lot faster and convenient for me.