You are talking about the Gigabyte GA-965P-DS3, right?
It has 6
SATA ports on the board (3 sets of 2). 4 are controlled by the ICH8 southbridge (orange), and the other 2 (purple, and referred to in the manual as the "GSATA" ports) are controlled by an extra controller on the board.
You can use whichever port you want, it really shouldn't matter. I used one of the ICH8-controlled ports.