I have tried to do the bathroom pass thing about a thousand different ways. Okay, I'm exaggerating. But some days I feel like it. No matter what there always seems to be a few who take advantage.
The best way I've figured out, is to create a pass they keep in their binder. If they would like to use the restroom, they bring me their pass and then I sign it. I give them 6 passes per 6 six weeks. They know that when they get their report card (we are on a six weeks schedule) they get a new pass.