How can I better control temperature differences between floors in my two story home that has two HVAC systems?
Leave the door - first and foremost, for fire safety, second, to keep from having all the cold air run downstairs and all the hot air run upstairs and then going nuts trying to keep any setting on either floor, especially if there isn't (would not expect with separate systems) a duct to circulate air between floors. If you have a door, you can let the lower floor warm up at night in cooling season, for instance, rather than needing to keep it "a few degrees cooler" to prevent warm air from rushing upstairs.

As for efficiency, heat or cool the part you are in when you are in it, and let it float warm in summer/cool in winter when you are not in it; just figure out how much the "lag time" is to get the place to temperature and start conditioning the space from your "warm AC" or "cool Heat" setting for when you are not there to the temperature you want it at when you are there far enough in advance so it's ready when you are.