There is no SATA 3.
It is either SATA.
SATA2 or SATA6.
If like my board it has a blue SATA2 connector on the board. It has 4 ports for four HD's to plug into. All internal HD's plug into it.
You are probably plugged into the e-SATA port for external hardrives. Select Config
If the above is your board the HD's plug in where the pics are marked with yellow highlight.
D-E on left
D-E Deluxe right.