Yes you can leave everything in filter's includeing sponges, def bio wheel, as well as ceramic pieces why you would be using carbon exsp in your doing normal water changes btw, I would be doing water changes while treating and replace and prazipro that you remove meaning if you have a 90 gallon tank and remove 40 gallon's of water after anding your safe you would be adding 2 tsp for 40 gallon's of water removed what are you using the prazipro too treat?