Refer to the motherboard manual.
Chapter 2: BIOS information
Enter the BIOS by pressing Delete when you power your system up. You should now see the main menu, as shown in Chapter 2.3. The option you require is IDE Configuration, and the sub-option is SMART Monitoring [Auto]. By default, this is set as Auto on this motherboard, however explicitly set it to Enabled and then save changes by pressing F10.
Reboot, and see if SMART is now available.
Edit: As regards the ports in use, it should make no difference. They're all created equal. I've had to do that in the past, purely and simply because of the location of some of the sockets (they were obscured when a graphics card was installed).