Betta with fin rot.....water change?

I figured out that my betta has fin rot. I got him Maracyn2 and have been treating him for 2 days. I also took out all the gravel and fake plant so his tank is now completely bare except for the filter. I have been treating the water with aquarium salt and I got purified water just in case. I have noticed all the poop on the bottom after just 2 days....should I clean this up?? I don't want it to make the water worse and make the fin rot worse. Also, how often/how much water should I be changing when I'm medicating? Any advice would be helpful! Thanks!Betta with fin rot.....water change?when ya are changing your water 20 % would be fine each week maybe do one extra when using the medicine.if ya have a carbon filter in your filter change it as this is what takes out the medicine in the water.as for that there is not to much other than keeping tank clean (gravel) without changing to much water.keep using the treatment.good luck.Betta with fin rot.....water change?if your filter has charcoal in it remove that to it catches treatment