It depends on the RAID type you use. I don't fully understand it my self, all I know is that I can do it with my motherboard
But 1 type of raid will still work even if the second drive goes down.
I have also heard that using RAID it will downsize the biggest drive to match the smallest one on the setup - Don't know if that is true or not.
I wouldn't merge the 2 drives together - it will help keep things seperate if they have different drive letters.
Plus if you fill up the data drive you won't have to worry about it carrying over and filling up your windows drive.