I put the chamomile in a hanging hop spider - see pic. They should be treated like any other hop addition to the boil. Put them in a hop bag or something similar. I'm sure that none of the chamomile got into my fermentor.
BTW, I still have bottles of this. I found one a week ago and it was still very nice. The chamomile is not strong in mine, and the honey is recognizable but just barely.