Yes and no. No HD, SATA II or SATA III, can't pull data off the spinning platters at a rate anywhere near 3 GB/s ..... however, your HD cache is essentially a small SSD. So transfers back and forth from cache will in fact benefit from a 6 GB/s connection.
Is there something else ya wanna connect to that 2nd SATA III port ? If not, connect the SSD and HD to the SATA III ports.