The problem with that large of a quarantine system is that the cost of some chemicals will become prohibitive - praziquantel for instance. You'll want to do as wooden-reefer says and have a very active biofilter going so that you can batch quarantine a group of fish at once, in order to save time and expense.
My general suggestion is to quarantine the fish for six weeks, and during that time, treat them twice with praziquantel at 2ppm and either run coppersafe the whole time, or run an ionic copper treatment at 0.20ppm for 14 days. Obviously, there is more to it than that, some fish are sensitive to copper, etc.
Jay