It looks like you are using a single zone setpoint manager. If you select that object and look in the editor there is a field for control zone, which can only be one of your thermal zones, ideally the lone located where the thermostat will be. It looks like you are using constant volume air terminals without reheat, so the other zones have no way alter the amount of conditioning. Since external and possibly internal loads vary throughout time, there isn't a specific size of the terminals that will keep it balanced. If it is appropriate based on how these zones are connected, you could add in some air mixing objects between the zones.