Can I make a RAID set over all 6 ports on the new X9Sxx mainboards with Sata-2 and Sata-3 capability?
Or do I need to make a RAID set over the SATA-3 ports and another one over the SATA-2 ports?
No, you cannot make 1 raid volume. These are 2 separate controllers, you can configure raid over the sata2 controller, and configure raid over the sata 3 controller.