Temporarily remove the filter while you clean it since you don't have it running anyways. The only reason why your not running the filter is so that the filtration system won't clean out the medication. I may let the filteration system run for an hour AFTER adding the medication so it can have the medication in it's system while it is sitting there.
Mythlene Blue is a common additive for illness and can be used for a variety of illnesses. It worked great for my Betta and other fish. It is critical that you buy Aquarium salt and do NOT use table salt or other salt like products. Aquarium salt is always good to have on hand and add to the water. Just don't oversalt. I would also add some Stress Coat to the water after they get well or after a complete water change. Helps them deal with the stress of the situation. Always add the stuff when adding new fish as well.
Good luck! Hope they get better soon!!!