I may have missed it but did you ever answer if you tank was cycled when you added the guppies??? If it wasn't, that could be the cause and I don't know that any medication will help. If it was cycled, I agree that you should only treat the ill fish, not necessarily the entire tank if no one else is ill.
As for the filter, you need to take the charcoal out if you put medicine in or else the medicine won't work. When I change my filter pad every few months I put a new one in on top of the old one first for a week or two then take the old one out. I am not familiar with your type of filter to know if this is an option for you. The bacteria in the substrate and on your plants and decorations will help, too. Good luck
As for the filter, you need to take the charcoal out if you put medicine in or else the medicine won't work. When I change my filter pad every few months I put a new one in on top of the old one first for a week or two then take the old one out. I am not familiar with your type of filter to know if this is an option for you. The bacteria in the substrate and on your plants and decorations will help, too. Good luck