My babies have parasites!

We took Skooter and Rocco to the vet today to have checkups. Rocco had a fecal done by a different vet a long time ago and supposedly was fantastic. The vet said they both looked great and our set up for their cages were perfect and when we left she said she would get back to me with the results from the fecal. They both have coccidia and little Skooter has pinworms. She thinks they both contracted these from the petstore. Not sure how Rocco got coccidia if his fecal was fine when we got him a year ago. But anyway, she told us up front she was a general practioner and not a reptile expert. I am having major difficulties finding a reptile expert thats even remotely close to us. So she was consulting with an expert that she uses frequently to find out exactly how to treat my babies. Im sure many of you have had experience with this so if you dont mind I would love to hear about your experiences and any suggestions you have i would grealty appreciate. Oh, Rocco and Skooter have never been introduced so im quite sure Rocco did not get coccidia from her. I have Skooter on reptile carpet right now because she is so small but I think im going to change her to paper towels until we get rid of these parasites so I can change them daily. Thanks everyone for your help and advice if you have any!
Jenn, Rocco, and Skooter