TL;DR; It does not matter much. Either way will be about as fast.
Somewhat more detailed:
The HDD will not profit from being on a SATA III bus. Max sequential speed from a consumer SATA disk is about 100MiB/sec. Max speed from a high performance 15K RPM SAS drives on the outer track is up to 200MiB/sec. Both speeds will not even fill a SATA II connection.
A modern SSD however can use more than SATA II speeds and will be faster on a SATA III bus. THe difference might not be all that large unless you are doing sequential transfers, which is unlikely on a small SSD with the OS on it.
In practise this means you should put the SSD on the SATA III port and you might see s light speed gain. (Remember, the SATA-bus channels is max speeds, and usually not sustained speeds).