Hi Chisnfips,
With regard to your carbon filter, as sunflower and hellohefalump have said you do need to remove a carbon filter when treating with meds.
When using a carbon filter it needs to be renewed every 4-6 weeks, it can not be cleaned or washed out it must be renewed.
There is a lot of controversy over carbon filters, some people say that they do not work after the first two weeks and some people are worried that they may leak chemicals back into the tank.
If a carbon filter is left longer that the recommended time it will start leaking the chemicals it has removed back into the tank, so although the manufacturers, (in my case) say 4-6 weeks, I personally always change mine after 4 weeks (just to be safe).
I have been told that if you remove the carbon filter after, say one week (because of treating with meds), as long as you keep it in a bag and it stays wet you can put the same carbon filter back in the tank, but the "4 weeks" does not start again, you only have 3 weeks of use left. Although I have been assured this is correct, I personally have not felt confident to do this, and if I have removed a carbon because of meds I have thrown it away and started next time with a fresh one.
Possibly it is a waste, but for me its better safe than sorry.
Good luck with your treatments, hope the fish feel better soon