Having some problems with my tank with parameters out of whack. I transferred both of my clowns to a large measuring cup until I get the issues resolved. I used bottled spring water and matched the salinity from my tank. My parameters are decent for most part except ammonia which is a bit high. I don't think they are breathing heavy because of the ammonia though because this morning when I first poured water it was yellow which reads at 0 ppm. I keep oxygenating the water but doesnt seem to help. Temperature is at 80 degrees. I keep my tank at that temp and they did just fine. I'm not sure how to get them to stop breathing so heavy.
Welcome to Reef2Reef!
Fish can breath rapidly from a variety of reasons, and not all are related to water quality or dissolved oxygen. First off - are there any other animals in the tank? Snails, shrimp, crabs, etc.? If so and if they are doing well, that can be used as a diagnostic tool that points less at water issues and more to gill disease in the fish (since the invertebrates don't catch fish diseases). If you don't have any other animals in the tank it doesn't rule out gill disease here, just makes it harder to diagnose.
Holding the fish in the cup is not the best. Better would be to identify the water quality issues in the tank and correct them (ammonia detoxifiers, etc.). Adding aeration would be the only thing I see that might be an issue.
Ultimately, this is likely a gill disease and is possibly velvet (Amyloodinium). I hope not because treating that isn't going to be possible in the tank you have, and it kills fish very quickly, so you likely won't have time to set up a treatment tank.
Worst case scenario is you won't be able to save the clownfish. What I would do is let the tank run for a couple of weeks and then add some hardy invertebrates. If they do well, then add a few more and just run the tank with those animals for 60+ days. Then, you can try fish again. If possible, buy pre quarantined fish.
Good luck!
Jay