How to control both CO2 concentration and ventilation schedule in EMS?

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If you have two programs that are trying to change something about a window, then EnergyPlus will execute the program code in the order listed by the Program Calling Manager object. So, you should be able to define two programs and list them both. You could also define one program that uses all the sensors and other EMS components to apply your desired CO2 and night ventilation strategies.

You need to define multiple EMS sensors to measure outputs calculated by EnergyPlus (i.e. one sensor for each zone you want to measure CO2 concentration) and multiple EMS actuators to define what you want to override (i.e. one actuator for each window that you want to open or close). If you have access to DesignBuilder (an interface for EnergyPlus), it has a scripting module that can use loops to automatically create all sensors or actuators you want for a given variable -- you don't have to define all the window names or zone names.