I have the Fractal R5. I don't use any fans on the top - I don't like them there as I set my other keyboard on top of the case.
I have the two stock fans in the front, drawing in. One fan on the bottom, in front of the power supply, drawing in. This fan seems to have the best effect on the GPU. Then I have the fan on the back by the CPU as the only exhaust. This blows through my Corsair H90 radiator. Well, the PSU is exhaust, too. All the inlets are filtered.