Just plug in a schedule to the "ooeningAreaFractionalSch_" input of the "Set EP Airflow" component.
To have two windows treated differently, you'll probably want to use two "setEPAirflow" components in tandem and have each component correspond to a different window. You will probably want to use natVentType 2 (custom wind and stack object) so that you can control the operable area and normal vector assigned to each window.