I recently bought a new motherboard that has one SATA 6Gb/s port and multiple SATA 3 Gb/s ports. I will connect four things to it - two hard drives, one optical drive and one eSATA front panel connector. Both of the hard drives do not support speeds of 6 Gb/s, and naturally the same is with the optical drive.
So my question is - would there be any advantages to connecting a 3 Gb/s hard disk to a 6 Gb/s port, as opposed to a 3 Gb/s port? After all, the 6Gb/s standard has more to it than just the transfer rate improvement - it has support for better power management, isochronous data transfers etc. Also, would the existing eSATA port on the front panel of the chassis (which was created before the 6 Gb/s standard) receive the benefit of increased bandwidth from being connected to a 6 Gb/s port?
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More aboutsata feature backward compatibility
Basically no, it will make little to no difference at all. Put a sata III ssd on one of the 6GB ports, and use the rest for whatever else you need to connect.
You will get no benefit from hooking a Sata II device to a sata III port.