There are HDD's with SATA3 out right now. And there are SATA2 SSD's out, which is becoming old news fast. If its SATA2 use SATA3 if you have some to spare, if its SATA3 use SATA3. Thats usually my build rule.
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.