Ok, so with leaving SATA mode in AHCI, I boot right up, and in looking in Windows Disk Manager it see's the 100GB volume and the 1200ishGB volume I made under RAID configuration. So, whats happening if SATA mode is set to AHCI, but Windows still see's the RAID volumes I created, is it still writing to both drives?
Ok, so after a little more time on Google I found this, and it worked, I am now booting to the RAID volume and the two volumes show in the rapid storage tech application.
Here's a link, it uses a util called RAIDfix, or you can modify the registry yourself. I chose the util.