Hello, how would you suggest I set the 2 separate thermostats for the upstairs and downstairs. There is 1 stairway door between them and the downstairs is below ground level with a walkout door. Is it better in the winter to set the upstairs at a higher temperature than the downstairs or vice versa? What about a/c weather which is better setting?

Heat rises, it doesn't matter if it is winter or summer time. So if you set the downstairs lower, in the winter, than the upstairs the upstairs should naturally stay warmer than the downstairs. Just the opposite in the in the summer time. If you set the downstairs cooler than the upstairs the cool air is going to stay in the lower part of the house.
So I say set the downstairs comfortable at a comfortable temp and then set the upstairs at a temp that makes it comfortable.