In nearly all situations, the best way to setup fans is to have 1 or 2 (2 is better) pulling cool air in at the front. And 1 fan pulling the warm air out the back. This creates a natural flow of air that flows through your system picking up the warm air that is moving off of your CPU and GPU.
By adding a side fan, you interrupt that natural flow, and can actually create "hot" pockets of air within the case, something that is not desirable.