i have a 5 or 6 inch fantail that has had finrot for about four weeks.
for two weeks i treated him in his normal 33gal tank with melafix and pimafix. and i followed the directions as listed (removed carbon, used appropriate amount of meds, water changes every seven days) and it still wasn't clearing up so i moved him to a 10gal hospital tank. i continue to use melafix and i now add maracyn. i am supposed to let the meds build up (again i think i am supposed to do water changes once a week) but since the meds kill all the benificial bacteria ammonia builds up really fast. i have to do water changes about every two or three days even when using ammonia lock.

all the water tests have been within the normal range for the 33gal tank.
in the 10gal the ammonia should be netralized (up to 3ppm i think) but the results always come back showing between 2-4ppm.
other than the ammonia everything has been in a normal range.
i use the aquaclear 50 filter for both the 33gal and the 10gal.

i am concerned that if i don't let the meds build up he will never heal and i will create a super bacteria but i can't have the ammonia levels rise. i don't know what to do.

You do not have the 10 gallon tank cycled, I gather. Maracyn I or II does not do too much to the cycle of an established tank. Occasionally it may bump it a bit, but rarely do that kind of damage.

Since you have an uncycled tank, you are going to have to do drastic water changes here at the beginning to get the ammonia under control. Frankly, I would drain the tank and start again. It is such a small amount of water in a 10 gallon tank.

Refill the tank with fresh treated water. Make sure you have no carbon in your filter. Run the filter. Treat with Maracyn. Test your water each day. I would suggest just planning on a water change each day. The renewed medications you add each day will do the job. It is not a "buildup" of the meds that they are looking for - those directions are because most people do not do water changes very often - and would leave the change until the end of treatment. The directions are a way to get people to change the water MORE, not less. So do not be afraid to change out what you need to change each and every day to keep the ammonia under control between treatments. Change out 7 gallons and add the Maracyn. Add in some PRime or Amquel, also, if you can. It will tide the water over until your next change.

Having Maracyn work is great. But it really will not help if the water is so bad that it causes more problems.

So:

Change out enough water to get the ammonia down to under 0.25ppm.

Add your Maracyn. Add some Prime.

Test the water the next day. If the ammonia is 0.50 or over, change the water again to get the ammonia below 0.25. The add the next dose of Maracyn and some Prime.

Repeat treatment....

The AquaClear 50 pumps 200 gph. This is fine - GREAT for a 10-15 gallon tank. It is a bit underpowered for a 33 gallon tank. You should have at least 10 Times turnover an hour on a tank - a 33 gallon tank would need at least 330 gallons per hour turnover. I like to aim a bit higher. I would recommend adding another filter to the larger tank or buying a new filter (Emperor 400 or some such) for the 33 gallon tank and keeping the AquaClear 50 on the smaller tank....

Aww, you're such a nice fish keeper and your fish are lucky to have you as their fishkeeper cause you care so much and try to help, I sure hope they are lucky to survive through this...