Jeez, I am not sure James - all the raid that I have set up have been via scsi controller cards but I would think they would both be master...someone please correct me if I am wrong....
I guess with 2 drives you're just setting up mirroring?
While this guide is written for an MSI board it gives a good basic raid set up guide. Beware, been there with both stripe and mirror.......still recovering from a hd crash on the stripe array.