Beneficial Bacteria. Depending on the type of your filter, you may need to turn it off. Your goal is basically to keep the bacteria at least submerged in the tank water at all times. If this means turning your filter off and throwing the media (sponges, wool, etc.) in to the tank to float, then by all means, do it. Certain filters (such as hang-on-back AquaClear) can be left running up to a certain point. The important thing to remember is if the filter is left to dry, you will have to re-start your cycling process -- not fun. Please always keep your filter in tank water during maintenance.
Ahhh just read that bit, i never knew this