I have dual zone heating/ac in my home. In the winter, is it best to have the second floor set higher and the first floor lower or vice versa? When summer comes, the same question. Second floor set a bit lower than the first floor?

Hot air rises so setting the upstairs higher will make it even hotter. Best bet is to set the temperature where you are located to your comfortable temperature. Most peolple set the sleeping levels a couple of degrees lower than the living level.