Hello, I Have Been Using A Bipap For About A

Hello, I have been using a bipap for about a year, and often wake up coughing, gaging, spitting up yellow, chunky flem, there is a rattling noise in my throat when I breathe. My pulmonary doctor said my lungs are clear and to use Ventolin inhaler as needed and Resimat inhaler 2 puffs once a day. I still can't get any relief. Do you have any suggestions? Thank-you for your help. Mike