The most important rule is to open enough window to let fan breathe in all the air it wants. That means opening the windows to at least equal the size of the shutter hole when running the fan at high speed and about 2/3 that size when running the fan on low speed. That usually means 4, 6 or 9 square feet of open window. Remember: the fewer windows that are open, the stronger the breeze that comes through them.
Open whichever windows give you the most benefit. When it is cool outside, open any window to get a cool breeze. When it is hot outside, open the basement windows, or windows on the cool side of the house. You can also water the vegetation by a window, then pull the air through, using the fan as a type of swamp cooler.
At night, you will probably want to open the bedroom windows a short time before you are ready for bed. You will walk into a cool bedroom. Set the shut off timer so you do not get too cold at night.