I just bought an ASUS P5Q Pro. The board supports RAID which I do not intend to use at the moment. I currently have 2 SATA hard drives. one w/ os and other has just files. Im not sure as to which SATA port to plug it into since there are 6 RED ports, a WHITE and an ORANGE port.
You can use any of the red ports, which are all controlled by the Intel chipset. Although it makes no difference, the numbering of these ports (1-6) is on page 2-27 of the owners manual. The white and orange ports are controlled by the Silicon Image controller. It may be different on your board, but when I used the second controller on my (totally different) board there was a significant delay at startup while it was initialized.