To maintain the bacteria bed I always rinse my filter media out in water syphoned from the tank but I dispose of the solid waste in the bottom of the filter canister. I think keeping the bacteria that is living on the filter media intact is what's important.
Bear in mind that if your tank is a decent size and has been established for a while there will be a lot of bacteria in the tank anyway so you shouldn't upset the cycled status just bt swapping filters.
Keep an eye on the water chemistry anyway for a while to make sure everythin gis OK but I don't forsee a problem.