How big is your tank? Is it planted? In a well cycled tank, the good bacteria will live in the gravel, on the tank decorations, as well as in the filter media. Most filters have a little extra room to shove some extra filter floss or a sponge down into it. If you're worried about losing the bacteria, you can always add a sponge or a bit of filter floss into the filter and leave it in there, bacteria will grow on it, so that when you change your filter media you still have a good supply of the bacteria.
If you're due for a filter change soon here is a great option for you.
When you remove your old filter, keep it wet in a bit of aquarium water. After putting in your new filter, take a pair scissors and cut the old filter floss away from the old filter media. Remove any loose pieces of carbon from the floss then shove it down behind the new filter media or in front, where ever you have room for it. Beware, when you do this, the water in your tank may become a bit cloudy from squishing the filter floss, which is full of gunky stuff. This is also a great way to help jump start the cycle of a new tank
