If your tank doesn't have that many fish, you can continue using the top filter. Of course, good husbandry is to change water weekly. The nitrifying bacteria that accummulates in your bioballs are the good guys who'll eat up all those nitrites (which are toxic to your fish) and convert them to nitrates (gas which is harmless to a certain extent). If you have plants, then the nitrates will be good for them.

Yes, when changing water, you can leave the fish in the tank. Just be careful you don't suck them out by accident!