Yea that was my plan is to keep the rock in QT tank. OK, I'll start treating the clowns with Copper this weekend. Do I need to take out the carbon from the filters?
Yup.
Just follow the instructions on the bottle. Although I've been told to go 'slower' then their instructions. (If they say add 40 drops on day 1, add instead 20 drops then add 20 more the next day kind of thing). This helps build it up slower and gives the fish a more gradual time to adjust.
That being said, clownfish are hardy to copper. Mine barely reacted all to the copper in the tank, while some of the other fish got rather lethargic for a few days.