Unless you have an enclosed stairway with a door on it, the upstairs will ALWAYS be hotter than the downstairs. Warm air rises and it will accumulate upstairs, while the cooler air from the upstairs flows down to the first floor. It is simple physics and the only way to minimize it would be for the first floor's return duct to draw air from the second floor's ceiling where all the hot air is. It has little to do with register air flow. There is no way for the lower level's unit to circulate, or keep, its air away from the second floor.