I'm sure you've figured this out by now, but you can't change the SATA controller type on your boot drive. You need to enable dual SATA mode in the BIOS (RAID+IDE) and plug the boot disk into port SATA3_5. Then, you can setup raid on ports SATA3_1-4. Just be sure to set the primary boot disk to SATA3_5.
Thanks monza. I eventually figured that out, after plenty of trial and error. I've had this rig running for about 5 months now, with the only stability issue being occasional random reboots. I think that's due to a faulty boot drive, but I can't prove it.