The best way to cool down a 2-story house with a fan is to take a square-shaped fan and place it on the window sill of an upstairs window so that it blows outward. Next, try seal the area around the fan so that when it blows it will draw air from within the house and not outside air from the window in which it is positioned. This can be accomplished by partially closing the window so that it wedges the fan in place. A piece of cardboard could be positioned on top of the fan to cover the gap between the top of the fan and the window opening.
Next, close all the windows & doors in your house except for the the sliding glass back door (or a large window) down stairs. Leave it wide open.
Then go back up stairs and turn on your fan. Within minutes you should feel the cool air being sucked in from the back door down stairs. Your whole house cools quickly this way, provided that it is cool outside, like at night.
However, be careful. If you have a really well-sealed house and your fan is nicely sealed in the window frame, then if you forget to open the back door you may draw a large vacuum on your house and break a window!