Well SATA arent plug and play devices. Neither is raid. So when you first install windows and that blue screen comes up, you need to puch F6 to install third party device drivers. You should have gotten these with the drives/motherboard (for raid), but if not you will be able to downlaod them from the manufacturers website.
Then put them o na floppy and install them when windows first loads up and it will detect them from then on.
There is a good guide to setting up SATA at the top of this page. read it.
hope this helps