I Have Acid Reflux That Has Not Flared Up In

I have acid reflux that has not flared up in years, i.e., given me any noticeable symptoms. My gastroenterologist gave me a prescriptio for Protonix today. My throat was "angry red" when she saw me. I asked if it could be due to the acid reflux and she said yes. In the meantime, I do not know how to deal with the pain. It hurts all of the time, not just when I swallow and both ears hurt internally as well.
What can I do?