I buy the cheap replacement FX5 sponges off of amazon. It's like $20 for 12 of them. I will run a set for 3 months or so, once they become a pain to rinse I'll toss a new pair in. You kill some beneficial bacteria when doing a cleaning, but any bio media should be rinsed in tank water. Keep a basket full of bio media and set it aside. As long as you don't kill the bacteria on it, you should have no issues with the smaller amount killed off by rinsing the rest of the filter.
