You want cool air to intake front the bottom front and flow unobstructed to the top rear for exhaust. Since heat rises, this is the most logical fan setup and is frequently echoed by many veterans. You don't want too many high cfm fans or too many fans in the center of the case. This can negate your goals of optimal cooling. I don't like side fans too much in my builds, but if I were to use one, it would be a 200mm fan with lower cfm. I would rather position my aftermarket CPU fan blowing down toward the GPU and have the side fan exhausting all of that heat. It's much more logical.

If you'r gpu is not a reference design (read: blower) cooler, then setting the side panel to exhaust is normally better than intake.