the top PCIE slot is for your card, and the bottom slot is for the paddle card.
You have to put that paddle card in slave PCIEx16 slot i.e. nearer to the CPU and then place your graphic card in the Master PCIEx16 slot whichis nearer to the USB header,JPANEL headers etc.
if you have that correct then try this:
In the BIOS, under Advanced Chipset Settings, select AMD 790GX config., and set "Internal Graphics Mode Config" to "Disable."
Now select "PCI Express Confg." and select "Port #02 Features." Set "Gen2 High Speed Mode" to "Advertised RC".
Save and Exit. You should now be running at 16X.