Hi, Stacey,
my husband had the same problem with scatter from the radidation. Don't worrry about the radiation to the cancerous areas - that is getting there just fine.

In the case of an unknown primary, they should be radiating the best guess of where the primary is / was. You can verify with the RO that the tonsillar area was also zapped.

This was about the time when fatigue set in with my husband, too. It is a tough road, but I am sure you will get throught it together. Nutrition and hydration is key - you want to get the the TX as close to schedule as possible!
Maria