How many windows do I need to leave open? Which ones? How Far?

Opening two or more windows half way or more is recommended. Basically you should make it easy for the fan to pull in air. As for which windows to open, for general cooling you want to open windows far away from the fan to provide airflow to the entire house. Or, you can open windows in the areas you want cooled. For example, if the upstairs bedrooms are the warmest then open the windows in those rooms only and close the down stairs windows.