I agree about the separation. If he has myco, the other rats have already been exposed, so it's too late to save them from it by separating the sick rat. If the others have strong immune systems, they may not even present symptoms and may be fine. Just keep an eye on all of them.
I remember the first time one of our rats got myco, we were told to separate. It was so heart-breaking. They would stick their little arms out of the cage and try to reach for each other. I don't bother separating any more.
As for medicating, we've never had any problems. They take the Baytrill like it's candy. Just fill the syringe to the correct amount, and hold it in front of the rat, and let him take a taste. If all goes well, he'll just lap it up and all you have to do is push the plunger very slowly until it's all gone. If that doesn't work, you'll have to hold the rat wrapped in a towel and prop the side of his mouth open with the end of the syringe, and slowly squirt the Baytill in, a few drops at a time. The vet technician should have showed you how to do this.