I just recently purchased a Ecobee thermostat. And after a couple days of installing, I was told to set the thermostat to Auto. Which the Ecobee will do it's thing.
So to answer your question. The ecobee will only start your heater, and will heat your whole system. But will shut off when the zones with the sensors that are occupied have reached the temperature that was set on the thermostat. Meaning the heater will stay on until the rooms with the sensors have reached its comfort setting. Even if the rooms without the sensors have not reached the comfort setting you set the thermostat to. That would be because the ecobee does not know the rest of the rooms temperature without the sensors. So if you have the smartsensor in your master bedroom and are only occupying that room. And not occupying the room that you have the thermostat. and you set the thermostat to 72 degrees. And the current temperature is reading 72 degrees in the bedroom and 69 in the room with the thermostat. Then your heater will not start because there's no sense in starting the heater if the room that is being occupied is already at it's comfort setting.
Hope that helps