Ok, you lost me. Your board has two SATA controllers, the main one that is part of the Intel X79 PCH chipset, and the Marvell 9128 (kinda, sorta, not really) SATA III controller. They are independent of each other, are configured separately and differently, and have their own drivers.
If you disable the Marvell controller, regardless of mode, it will not function, period.
If you disable the Marvell controller, the Intel controller will still be functioning normally, regardless of the mode, AHCI, RAID, or IDE (yuck.) Two ports at 6Gb/s each, and four ports at 3Gb/s each.
