Hey Smooph -
Did you find the configuration? I have a custom built PC and the Intel Rapid Storage Technology program tells me all my SATA ports are internal. However, I wired up two of them to external ports on my chassis (eSATA). I want the software to recognize that the ports are external because then Windows will provide the "safely remove" option when a drive is plugged into one of those ports.
I tried to find the configuration in the registry but it doesn't seem to be in there. The info might be in the DMI data stored on the motherboard too. I plan to keep looking.
Looks like the ICH9/10 driver gets the configuration directly from the AHCI registers (CAP and PxCMD) inside the ICH9/10. They are write-once registers, and I would guess they are initialized by system BIOS after reset. So if your BIOS doesn't offer the choice of internal/external for each SATA port on the motherboard, then you're out of luck (like I am). I may complain to ASUS and beg for a new BIOS release, but somehow I don't expect to get very far.