How do I handle a up and down duplex with only 1 furnace and 1 thermostat. 

Blame the programmer.

You can loop them into separate thermostats so you can be pretty specific about individual rooms and temperature without adding a ton of cost so long as you don't go overboard.

In both I cover the gas for heat- I have the Chicago control thermostats on and the buildings are well insulated (one more than the other).

Unfortunately Nest only allows you to control two thermostats with one account. 

After the request was turned in a received an email from one of the programmers that asked me a few more questions and told me how much it would be.

They'll also replace every light in the property with LEDs and give you programmable thermostats and energy saving power strips at no cost.I don't know if they have a different program for MFRs, but at least give them a call.

But we have installed a small under-the-counter style refrigerator, microwave & coffee maker (just like a hotel room.)The biggest obstacle is that the house only has one thermostat, located upstairs.

Sometimes she changes light bulbs and replaces batteries in remotes and thermostats. 

Avery Carl - what thermostat do you use?