What kind of filter do you have? If it is one with a BIO-Wheel then you don't really need to worry about losing bacteria colonies when you change the filter carrtridge. If your filter has several types of media in it (i.e. sponge and biological material) then changing one won't hurt because the other will still provide a bacterial growth medium.
Gene Heitman - 12 tanks (11 freshwater and 1 saltwater), 206 gallons, 20+ species of fish/shrimp/snails, 52+ species of plants ... 10 years ago I just wanted 1 tank with some fish