I do have a motherboard with onboard too (Gigabyte GA-MA78G-DS3H) and I can't use two cards. My second PCIe slot does not work with video cards. Either it activates the one in the first PCIe slot, or the onboard if its missing.
I don't know about your specific mainboard, but I needed to buy a new one.
Have you tried dummy plugs?
I've heard many people use the onboard video to drive the monitor and use the other slots to mine. It's supposed to speed up mining as doesn't have to draw the screen.