You need both connections.
The psu will have sata power connectors. Connect one to each drive. It will fit only one way.
The sata signal cables have identical ends. They also fit only one way. Connect one end to the motherboard sata port, and the other end to the drive sata port. It does not matter if you use a 3gb or a 6gb sata port. I would pick a 3gb port, reserving a 6gb port for a ssd which is the only current device that can fully utilize 6gb.
You will have to do this for your hard drive or ssd also.