You will learn how often to change these with your feeding schedual and population densities. I hope this will help you. I have started using a sponge in the end of my Python tube while siphoning tanks to do water changes. When putting the water back into the tank I put one hand under the Python and let the water run off my hand and that way it isn't splashing directly into the tank causing problems for the young fry. If the tank really needs a clean up job I use an airline hose and then just siphon the debris.
Most fry are smart enough to stay away from the tube.
Other than that, it is difficult to clean a tank with a lot of little fry in the tank. I use Hydro-sponges in my tanks and those are easy enough to just take out and rinse and then put back into the tank. I have found with a lot of my fry from many species, that some are more susceptible to water quality than others. I will already have a 10 gallon ready a week ahead of time for them. After a week the fry are added to the new tank.