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Much research has shown that acid reflux can effect sinuses and cause headaches. The usual recommendations are to identify and eliminate your trigger foods, wait a couple of hours after eating before lying down, and sleep elevated on a pillow that supports you on an even plane through the entire torso and elevates you 6-8".  It is important that you don't just prop your head on pillows or lie on too short a pillow.  Doing so just puts extra pressure on your stomach and makes everyting worse.  Make sure your pillow is at least 30" long - the 24" ones actually make problems worse.  In addition to helping your reflux by using gravity to keep acid down, sleeping elevated helps the sinuses drain and also helps with the headaches.