gosh, that sounds awful. since you don't know which one is worst, i'd say the individual cups is a good thing, but that may make it hard to portion out medication. i would keep them separate, clean out the entire tank, and keep each one quarantined until you're sure of health before reintroducing them to the full-sized tank. also, make sure that the water in those little cups is cleaned every day, especially if they're very tiny (the cups, i mean.) that much be a handful. i've heard good things about seachem's polyguard. i've used it myself and it's the only thing that got rid of my guy's finrot, although it keeps coming back. it does seem to knock it out for awhile. it's just a soak, not a tank additive, so you'd have to soak them in a bath of it every other day or so for about a week. i'm sorry that happened. good luck!