Different people have different definitions for what makes a thermostat "smart". To some people, that means being able to adjust it from a phone app or with Alexa, Nest has the philosophy that the thermostat should have built in "intelligence" that allows it to infer what the setpoint should be without the user having to enter the setpoint and/or a schedule. For others, it means being able to communicate with a hub like Hubitat which provides an opportunity for the homeowner to take advantage of all of the information from other sensors throughout the house to improve HVAC control. In that last category, the thermostat itself doesn't contribute the "smarts" but plays nicely in a "smart" system. The Zen thermostat, for example, has no scheduling capability by itself, but integrates nicely into a home automation system that can schedule setpoints using very sophisticated logic.
Your terminology is correct. You probably have a board called a zone controller near your air handler that receives the signals from the two thermostats and decides what commands to send to the air handler and to zone dampers. The common way to add smarts to such a system is to swap the thermostats for smart thermostats, using whatever definition you prefer, and let your zone controller continue to function as it does now. I have written a Hubitat app that replaces the zone controller itself. However, as noted below, I don't recommend that for you.
The fact that you mention emergency heat leads me to believe that your system is a heat pump system. My Hubitat zone control app does not yet support heat pump systems, although that is on my list of future enhancements. A lot of 2-stage systems get wired as 1-stage systems with the air handler itself deciding when to use 2nd stage. The usual logic is for it to go to 2nd stage after running for 10-12 minutes in 1st stage. That distinction doesn't really impact your thermostat choice.
With these goals, I recommend avoiding any thermostat that tries to put a lot of smarts in the thermostat product itself. Having the thermostat and Hubitat both trying to be in control is sort of like having two people both wanting to be in control. ZWave and Zigbee devices tend to fit better into a Hubitat system than devices which require cloud integrations, like Nest or Ecobee.
That would be a good choice.
I bought a Zen to test. My wife liked the aesthetics of it, so we ended up leaving it in place after the test and getting another one for a different zone. Setting up the Zen was a little more challenging than the other models I tested, but I'm pretty sure you will be able to set it up for your system.
