I have 1 heating/AC unit and 2 thermostats. 1 for the entire downstairs and 1 for the room above my garage. The duct for the upstairs room has a butterfly valve that I think is supposed to be controlled by the upstairs thermostat. The upstairs room is always warmer in the winter and cooler in the summer. How can I make it match the downstairs temp more closely? Does the valve need to be adjusted? How do I check it? Any help would be appreciated.

You have a zoned system and without being there it will be very difficult to tell you how to adjust it for proper operation. Contact someone local in the HVAC biz that has experience in zoned systems for a on site visit so it can be adjusted properly.