http://www.google.com/imgres?um=1&hl=en&safe=off&sa=N&biw=1366&bih=676&tbm=isch&tbnid=nzzQ-v6FemPKIM:&imgrefurl=http://www.legitreviews.com/news/14395/&docid=JOoRryR1wIfQtM&imgurl=http://www.legitreviews.com/images/reviews/news/z77-extreme6-tb4.jpg&w=480&h=295&ei=goVYUb2LI8ixiwKh_YDQDQ&zoom=1&ved=1t:3588,r:9,s:0,i:112&iact=rc&dur=5644&page=1&tbnh=176&tbnw=287&start=0&ndsp=17&tx=181&ty=65
Looking at that motherboard, it looks as though they put enough room between the PCIe x16 and the PCI slot for it to work. The configuration would be GPU, Audio Card, GPU and it looks as if the GPUs would both only cover up the PCIe x1 slots.
If this is not the same motherboard you're looking at or is a different model you could present a link to the one you're talking about and I can take a look at that one too. I know there are a variety of different chipsets on the same motherboard that occasionally come with different models that are labeled similarly.