I have an older machine based on an ASUS Rampage Formula and just got a new SATA III controller for the SSD I picked up. My motherboard has two PCI Express 2.0 slots (I used to run crossfire 4870s), and I was wondering if it would mess with my current ATI 6850 PCIx16 card if I were to place the SATA controller in the 2nd x16 slot. The PCI-E x1 slots with the card installed I have don't yield very good performance (around 160 MBPS).
According to the specifications for your motherboard, both PCI-E x16 slots can run in x16 mode at the same time. All PCI-E slots are 2.0. However, if the SATA III card is only set up for x1 mode, there will be no change in performance.