Well, if it is a bacterial fungus, you'll want to treat with antibiotics, I would also recommend a med for true fungus', just incase. The real problem is that while the antibiotics are working on the fish, they are also working on the biological filter your trying to encourage
Here are the options I see.
Remove to a quarantine tank, treat with E-mycin and Mardel's MarOxy, do daily 25% water changes on the q-tank to keep ammonia down. Treat for 5 days.
Treat in the display tank with the same method as above. The biological filter will probably be killed off and you'll be back to square one.
Treat in the display aquarium with a weak antibiotic that hasn't been credited with any biofilter crashes (like melafix) but also may not be strong enough to kill off the infection.
Let the fish try to fight off the infection itself (chances are poor), doing nothing, but reducing ammonia in the display tank.
Unfortunately all these option suck. All I can tell you is at some point in time, most of us have been right where you are now. This hobby is very rewarding, but occasionally it does have a down side. If there is any info we can give you to aid you in your decision, let us know.