ammonia burns

This is the only thing that I can think of that could be causing my goldfish
to suffer so and to look so bad. I don't know what else to do. I have been
doing frequent water changes, I changed the filter cartridge. I did have to
medicate the tank a while back with some Fungus clear medication. Did I
kill my good bacteria by doing that? What else should I be doing? All my
fishies are now all turning an ugly brown color and I think they are getting
very sick. They are feeding and swimming ok though. Please help me if you
can. I have no experience with gold fish, only with tropicals.

Thanks, Sarah