according to the MSI P965 Platinum specs, you have 2 onboard SATAII controller
"Serial ATAII controller integrated in ICH8R and JMicron JMB361
• Up to 300MB/s transfer speed
• Can connect up to 7 Serial ATA II drives (6 drives from ICH8R, 1 drive from JMB361)
• Supports ACHI controller with SATAII RAID 0, 1, 5 and 10 (ICH8R)
• Supports SATAII hot plug "
so you could just connect your sata hdd to the ICH8R (the purple one) sata port, then activate the JMB361 AHCI or RAID drive from your bios then install your driver in your os. after that shutdown your pc, switch your hdd to JMB361 Port (the blue one, only one below the orange pci slot), start your pc, activate the bios option for the ICH8R ACHI or RAID drive, save your settings then you can install the driver for your ICH8R port.
by the way if you only have one hdd, just use AHCI, if u have more, then it's up to you to use RAID or AHCI.