I had our letter (about three pages of legalese) notarized and had our pediatrician write a note on medical letterhead stating that the exemption had been reviewed and that we were in agreement, the pediatrician was confident in what had been discussed/agreed, and that further dialogue would take place if warranted.
I always keep that note/a copy of the note with our exemption letter. It's saved me from many a headache.
Something I would suggest, as I found out the hard way, is to be aware of specific laws. There was a chicken pox outbreak at my child's morning program, and I received a personal phone call where they tried to tell me that I needed to keep him home for two weeks. I said, "Well, I'd rather that my child contract it naturally!", they called the DPH, and they finally said that they couldn't prevent him from attending the program unless someone in his group contracted CP.
I had personal experience with the CP vaccine as a child that did not end well, and I decided early on that my child would not be receiving that vaccine. Why, yes, I will die on that hill.