Also changed furnace filters, and new batteries in the thermostat every other year.

Solar fan:PRO: doesn't run on electricity, no rodents, no moisture, fresh air CON: expensive $599 (covers up to 1200 sq ft) to $899 (covers up to 1600 sq ft) installedRooftop fan:PRO: cheaperCON: requires power and thermostat setting/can increase utility bills

Because the Thermostat is turned so low, a lot of condensation is forming on the ductwork inbetween the first floor ceiling and the second floor floor.  

They get the other 1/2 when the outside unit is installed, system is charged, thermostat installed and is cooling.Plumbing, they get 1/3 when the plumbing is roughed in, 1/3 when it's topped out and the final 1/3 when finish work is completed.My contractor doesn't even get his first draw until the house is up and felt/doors/windows/siding are installed.  

The furnace condensate line needs connected into the floor drain, and a temporary thermostat supplied.

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

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. 

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.