HDDs don't get any benefit from being on a SATA 6Gb/s port vs a SATA 3Gb/s port...except faster burst speed, but that doesn't really matter.
Plug the SSDs into the SATA 6Gb/s ports and anything else into the SATA 3Gb/s ports. If you get a PCIe card, plug the optical drive in that.
If you want full SATA 6Gb/s performance get a PCIe x4 card, not x1. They are like $60ish or so.