OptiMiser is limited to single zone modeling. You have two options for dealing with this.
1. You can model the zones as though they are separate units of a multi-unit building. This requires using multiple project files. The Multi-Family controls allow you to remove the boundary between the two zones from the thermal boundary.
2. You can calculate weighted averages for the thermostat set-points, using the % Load for each system as the weighting. In you case this would still specify a setback thermostat, but the setback would be reduced.