The article didn't talk about skimmer use, so entirely possible you can go ahead as usual. I don't know much about skimmers or what exactly they pull out of the water. Since it's only a 6 day treatment, I would probably err on the side of caution and turn it off. But if I knew more about what is skimmed from the water, I might be more confident in keeping it running or not. Turn off any UV you are running--that will degrade the cipro and diminish its effectiveness.