What equipment is used to switch the zones? Is it electronically controlled dampers or something else that's controlling the zone?
I have an Ecobee, but it's a single zone system. I love it, but there are a few small quirks to how the Ecobee operates. Understanding Home vs Away vs Resume Program are key. But I've automated it to my liking with Hubitat and Ecobee Suite app/drivers (see below).
There is an Ecobee Suite of apps and drivers that is very good. It's available here:
I used Ecobee Suite on SmartThings and now on Hubitat. The cool thing is the developer has really done a good job at making it a very robust set of features. Ecobee Suite has included a lot of use cases: setting the thermostats to Away or Home based on Hubitat mode, using smart vents to isolate heat/cold to one room or area of the house, work from home, etc....
There's a lot you can do, but I would start out slow. Get the thermostat(s) and then build the automation's one by one until you are happy. Most of the time the issue is whether there's a smart thermostat that can interface with your HVAC system. So I would start there to see if your options are limited. Even if they are limited to a specific smart thermostat, you should be able to make it smart using HE.