I also use MSI Afterburner, and the only stuff I mess with 99% of the time are the core and memory clocks; i.e. leave the GPU's fan control alone. Further, if you have a reference GPU i.e. single fan then yeah sure those will overheat easy.
In the BIOS you can ramp-up the fan profiles, but it won't do you any good if there's poor planning with airflow and/or the case is poorly ventilated.
My approach was a front/bottom (in ; 3x120's) and a top/rear (out 3x120's); my case also has a 240mm, but I'm even still trying to figure out (in or out).
Reference GPU (poor for OC):
http://images17.newegg.com/is/image/newegg/14-130-587-TS?$S300W$
Non-Reference GPU (better for OC):
http://images17.newegg.com/is/image/newegg/14-121-432-TS?$S300W$
Then there's putting GPU's side to side with no gaps...same problem.