Is the main floor insulated? Can you use the same type of insulation? Maybe the heating/cooling vents need to be looked at to make sure they are allowing free flowing heat/cold.
We don't have the separate garage so we don't notice the problem so much, but it is noticeable a little because the garage area doesn't have any heating vents. The vents stop in the kitchen/dining room area, so the living room/garage gets a little cool when it's cold outside, not so noticeable with the A/C since there are overhead ducting for the A/C.