I own that board, and the chipset fan is loud, however, if you use the bundled DFI smart guardian program you can manage the RPM and make the fan almost silent.
Just pop off the chipset heatsink, and replace the stock paste with some AS5, and your temps will lower ~10*C. Because of that you can then lower your RPM and you wont have any noise. Anyways thats my advice.
As for using the lower PCIe x16 slot, it will work but you need to move the jumpers into "dual card mode" and you will have your bandwidth halved to x8 speed. I for one would just throw some AS5 on the chipset, drop the RPM and use the x16 PCIe slot. At least thats what works for me.
EDIT: My chipset fan operates in the 2300-2900 RPM range, and my temps are 48*C idle, 53*C full load. They are on the high side, but the chipset fan is inaudible over my 7800GT and case fans. At full 5000+ RPM it is very loud and noticible.