Our new home of approximately 2000 sq. ft. has two heating sources, a heat pump for the upstairs and a gas furnace for the first floor. We do not have a basement. The stairway is open to a second floor loft with two bedrooms and a bath enclosed. I have set back thermostats on both heaters. I am trying to figure out how to run them. I keep our home at 68 degrees (in the winter) or around that when we are home and set it back when we are away and at night. Do I start the upstairs heat pump first to heat up the house then the downstairs? Do I make the upstairs a degree or two higher than the downstairs? Is the heating of the downstairs affected by the temperature of the upstairs and vice versa?

Heat rises so the upstirs will normally be warmer than down.

Heat rises that is what I would have thought. Right now the first floor is at 72 degrees and the second floor is at 69 degrees. That is why I asked the question.

If this is in cooling mode the downstairs can be affected by may things. Like more windows facing south or west, patio doors, doors opening and closing, kitchen stove, refrigerator,etc. In the heating mode the gas furnace will put out supply air at about 130 degrees and a heat pump about 90 degrees. You must compare apples to apples. You do have 2 different scources

Take a normal pool thermometer, or any other separate one, and let it sit in the first floor area for 20 minutes. Then, bring it to the second floor and do the same.

If the top one is warner than the bottom, this is normal.

Thermostats are not always accurate. They can be off by up to 5 degrees, so don't rely on them too much to find the exact temp in the house.