I am trying to even the temperature between downstairs and upstairs. I have multiple units, with multiple thermostats. I am concerned about energy usage. How can I best go about this?

Trial and error.

You can have the system balanced. This would require a manual D for duct design and would determine the air flow required for each space and air flow could be measured and set by placing an instrument on the discharge register and moving the dampers to set the proper air flow.

You can do an Manual D yourself by purchasing a program and you could buy a simple amemometer to set air flow.

Understanding Manual D (http://www.manuald.com/)