For future filter cleaning, here is what I do.
I have two containers of tank water. I place my sponges in one container and give them a squeeze, the dump that water and refill it again with more tank water from the second container and squeeze the filters again to make sure no loose particles are left... I don't squeeze that much, a few squeezes gets it all really. Then I take the filter casing (the plastic bit) and wash that thoroughly in tap water since that isn't what holds the bacteria and does get build up sometimes. Then re-assemble it and put it back in the tank. I just be careful to keep my sponges damp and only exposed to tank water, never tap water or water that hasn't first been dechlorinated.
You could try going to your fish shop and see if they can sell you some mature filter media that you could add to your filter to begin repopulating the bacteria.