Hi there,i am not too sure where you will find the onboard gpu settings in your bios,having never used Gigabyte boards,but you may have to dissable it as your using another gpu,to get the newest bios update,just go to the Gigabyte website,and find your board,then look for bios updates and download it.
Are you ok with flashing the bios,????
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AMD 965BE @4.032GHZ 24/7 VCORE 1.528v TEMPS 32C/52C
MSI 790FX GD70
3 X SAPPHIRE 4890 OC's 991/1100
4 GIG G-SKILL RIPJAWS 1600 @ 7 7 7 24 1.65v RUNNING @1680MHZ
4 SAMSUNG F1 750 GIG SATA II HDD's 2X RAID 0
THERMALTAKE ARMOR+ FULL TOWER CASE
THERMALTAKE TOUGHPOWER MODULAR 850W
THERMALTAKE BIGWATER 760IS WC
28" HANNS-G LCD 1920X1200 3ms
WINDOWS 7 ULTIMATE 32bit OS