Okay... we have two different media that we put into the filters - the first is Eheim Substrat Pro (biological) -The filter pads are fine to leave in. Just remove all media that is for chemical filtration, such as carbon, chem pure, those types of things. Also on the bottle it says that you can leave your skimmer on. I always turn it off when I uses Stop Parasites, It just overflows and skims out the med.