Integrated Peripherals
Intel Controller (Yellow Ports)
SATA RAID/AHCI Mode (Intel ICH10R Southbridge) ............. AHCI
SATA Port0-3 Native Mode ................................... Enabled (or Disabled, both will work)
Connect your hard drive with operating system to the first yellow port SATAII_0 (Against the PCB). Then connect your CD/DVD drive on the last Intel Yellow port SATA_5 against the PCB
As for the settings you mention, you can disable those if you are not using them, which it doesn't look like you need them if you only have 1 hard drive and one CD/DVD drive
Gigabyte/J.Micron Controller (Purple Ports)
Onboard SATA/IDE Device (GIGABYTE SATA2 Chip) ............. Disabled (Nothing connected to purple ports, so no need to enable
Onboard SATA/IDE Ctrl Mode (GIGABYTE SATA2 Chip) ........... IDE/AHCI/RAID = doesn't matter, disabled above