Good luck with the remaining chicks, hope they keep doing fine. I'd do what you are doing and just give them the amp if both it and the baytril are mixed in the water. As long as they are being medicated now the ones that feel fine should be fine, the sick ones will hopefully get better pretty fast, a day or two, but it may take the really sick ones a good week to act back to normal. Double check to be sure the really sick ones are drinking as they should be. The medicated water mixed with feed as Ten Chicks said is a good idea also.
Do be careful about cross contamination with your other chicks and chickens now, and even hatching eggs, since the oocysts are pretty darn tough.
Do be careful about cross contamination with your other chicks and chickens now, and even hatching eggs, since the oocysts are pretty darn tough.