My personal opinion is that there is enough bacteria in other places in the tank that it doesn't matter a whole lot if you replace filter media or kill the bacteria in the filter. This may be largely dependent on setup and stocking of the tank, and some may disagree.
I clean my filter media with a faucet every month and I've never had any nitrite or ammonia spikes after doing so.
As to how I clean it, I unhook everything and put it in the tub, pull everything out, rinse the filters in the sink, reassemble everything, and then clean the tub.