Setup BIOS onto new SDD Primary.

go to the tab with boot priority menu, and it should have a hardrive priority menu too, set your SSD first

BIOS talks to the motherboard directly and does not involve a hard drive or SSD at all so you are not running BIOS off a hard drive.

Did you unplug the extra hard drive while installing Windows on the SSD?

No I didn't unplug the old HDD when I installed windows on the new SSD. I am sure windows installed on the SSD though. The only real problem I am getting is it won't let me format the old HDD because the ASUS menu i get to by hitting 'Delete' on start up will not let me take the old HDD off as a backup boot drive. So when I try to switch permissions to format it says its a boot drive.