Treating displays with copper is a topic that has been debated heavily. From my experience treating my 250g FO system 3 (maybe 4) times with copper, I have not had any ammonia spikes, nor have I had issues with maintaining copper concentration levels despite heavy skimming. I keep a small sack of Cuprisorb in the sump to pick up any residual copper that might float around after treatment is done.
If I were to set up a quarantine tank big enough to treat all of my fish, then it would need to also be a 250g system with almost every piece of the same equipment, so I might as well just treat my existing system. I just keep a separate small QT for new incoming fish.
I have 200 pounds of sand in the display and coral skeletons for decoration. I've never had live rock so that may be an area that you could see some die off. For biofiltration I have 50+ liters of ceramic rings in the sump. The ceramic rings have never been affected by copper, they continue to process ammonia and nitrites as they always do. Many people actually use "seasoned" ceramic rings and live rock in their QT for biofiltration while treating with copper.
After the treatment is done, I do a big 50% water change and run carbon and cuprisorb. I always run carbon anyway since my tank is an FO so I don't need to worry about the carbon removing beneficial trace elements that corals need.
I highly recommend using Seachem's Cupramine, their copper test kit and also their Cuprisorb.
I keep my skimmer running while treating with Cupramine. Seachem also recommends it.
http://www.seachem.com/support/FAQs...mine.html#faq11
Q: I am treating my 90 Gallon tank with Cupramine. I've removed the activited charcoal and carbon and I turned off the UV and the Ozonizer. Shoud I turn off my Protein Skimmer?
A: It is perfectly acceptable and recommended to leave your skimmer on during treatment.
If you're concurrently treating with Prazi-Pro for flukes, then you will need to shut off the skimmer.
You will also need to turn off the UV sterilizer with both Cupramine and Prazi-Pro.