How to set the thermostat schedule to ThermostatSetpoint:SingleHeatingOrCooling instead of Dual Setpoint in Honeybee Energy

You can by using an OpenStudio Measure or a workflow like the one described here. But it is not natively supported by Honeybee schema.

The Day Schedule that gets used on the summer/winter design days is specifically the _summer_des_ and _winter_des_ schedules of the _base_schedule that you plug into the Seasonal Schedule. So just make sure that you are specifying the setpoints that you want on the _summer_des_ and _winter_des_ schedules when you create the _base_schedule with the Weekly Schedule component and the zone peaks should be as you expect.