With my ASUS board, the red sata was for the sata 2 and the black one was for the sata 3. Plug the red one into your hard drive / optical drive and find the plug them into those ( down right corner )http://www.pcstats.com/articleimages/200609/gbt945gms2_m.jpg
You have to plug also the sound, the fans, the usb, front panel on/off reset sound, if you have any, the ide cable, the 8 pin and the 24 pin on your motherboard.
I'm going to bed so if you have any question don't hesitate someone will come to the recue
Very good build by the way !