i believe that GPU has case exhaust to cool, but i am not positive. If that is true, then having your side fan as an exhaust fan is the way i would have also gone. if the fans on your GPU are rear exhaust fans (sucking from case out the back) then i would make the side fan an intake fan, so that the GPU gets fresh cool outside air. That is how my case is setup, and i noticed about a 3-4c difference from making the side fan an intake rather than exhaust.
as far as the fan speeds for your 2x 200mm fans, there is a speed control option in the BIOS that alllows you to set a fan profile for your onboard fans. I have mine all set to "performance" as this pushes the fans to 100%. there is a link on here explaining the BIOS options for different boards, what Mobo do you have and ill try to find the link for you.
-ASUS Rampage IV Extreme
-Intel i7-3930k @4.42GHz
-16GB CORSAIR DOMINATOR GT 2133MHz
-Corsair Force Series GT SSD 240GB
- 2x 3TB WD Caviar Black (RAID 1)
- XFX ProSeries 1250W PSU
-3x ASUS VE248Q 24" Monitor
- 2x XFX 7970R
- Xigmatek Elysium Black Case
- CORSAIR H100 CPU Cooler
- Logitech G500 Mouse