This is a bit of digression but I want to point out one thing.
Cycling with damsels is actually more effective than long term maintaining nitrification after cycle with a couple of damsels. Needless to day, a couple of damsles in a QT for months and months is pointless, unless you ghost feed excessive food all the time.
In cycling, at least by the damsels suffering, there will a an ACCUMULATION of ammonia because bacteria cannot catch up. This accumulation has some of the same effect of artificial ammonia pulse. Therefore, at the end of the cycle with damsels, there will be more bacteria than long term balance.
The same cannot be said of having a couple of damsels in a QT for months and months.
Couple things here.
One, as it sounds like we're not sure what we're treating, can we get a picture R.W. I will be up front in saying that most of my experience is in treating C. Irritans or "generic flukes", so if it is neither of those, I may not be of much help. If it is C. Irritans, I agree completely with Mr. Scribbled's advice, Cupramine has been a very effective and safe medication for me.
In regards to opinions on quarantine set ups. My advice to you is to do what best suits your needs and what you are most comfortable with. If you are building your fish population as I am/was, it may make sense for you to keep a cycled stable quarantine tank with a couple damsels - stable being the key here.
I have successfully quarantined two purple tilefish, a powder blue tang, a semilarvatus butterfly fish, a mitratus butterfly fish, a borbonius anthias, a black dog face pufferfish, and a potters angelfish doing this, thus my recommendation. Your call, but i've had good luck with this method and not lost any fish doing it this way - and there was no small sum of cash wrapped up in that group. I used a blue reef chromis and a sunshine chromis. I was never adding more than one or two fish at a time to be quarantined, so there was no ammonia spike.
I realized we've hijacked your thread now, and I apologize for that, but i'm not sure I agree regarding the use of artificial ammonia. If you are in fact "inexperienced" as Wooden Reefer assumed, balancing ammonia doses and measuring ammonia and nitrite on a daily basis may not be the most appealing chore for you and may be outside the scope of your abilities - though I personally doubt that as you have a decent collection of fish.
If you have a local fish store at your disposal, see if they'll loan or sell you a couple gallons of cycled bioballs and set up the wet dry. That will be more than enough nitrifying bacteria to handle the bioload. Monitor the ammonia and if for some reason it's not, just reduce feeding and supplement with water changes.
Lastly, regarding the pulse effect of dosing artificial ammonia. While it may be true that there will be a larger population initially, surely the bacterial colonies will regulate themselves to the available ammonia and nitrite and thus, any initial population surge will be reduced over a short amount of time rendering any initial benefit obsolete.
Food for thought.
