It's good that you are aware that you have got to be very careful when dealing with biological filtration, after all it is the lifeline of your tank and without it is, your fish would be swimming around in a toxic soup.
You mustn't let it worry you too much, as long as you are sensible and I'm not going to cause any damage to your biological filter. You can turn your filter for over an hour and as long as your media doesn't dry out, you're not going to lose all your bacteria. Obviously there are a few important rules you must follow, never wash your media out in tap water because chlorine will just destroy all the bacteria. And obviously I've already mentioned, don't let it dry out. When you are going to carry out maintenance on your filter, prepare yourself first, fill a bucket with existing tank water and make sure that you've got everything to hand. Obviously make sure you know how you are going to take the filter parts and where the different media goes.
When the top of the filter comes off take the tray or baskets that are holding the media and dunk them a few times in the bucket of water. If the trays are particularly dirty then you could use one of those strainers that you use with vegetables. I've got a metal one and when I used to have canister filters I would tip all the media into one and all the dirty water would drain out leaving the media. You don't want to go too mad cleaning it, just remove any solid debris and crap. It shouldn't take any longer than 20 minutes to clean a canister filter, your media will be perfectly okay during this time, just make sure that any media that you have just cleaned remains wet. I actually used to have two buckets of water at hand. I would use one bucket to clean the media, and the other bucket to store the newly clean media in so it wouldn't dry out.
As for any sponge or fibre media, just squeeze it out underneath the water until it is clean. The sponge media is normally only mechanical filtration so you can give this a good clean.
Don't worry about it, just follow those important steps and you'll be okay