The problem is that you need a functional OS for software implementations, but you don't have that on the moment you start that that OS.
So startting the OS on C: and the Raid on D: sounds normal to me. I never heard of some part of a disk used for installing the OS being not in the raid, while the remaing part of the same disk is part of the raid. As I understood this in not possible, all disks should be of equal size.
On the other hand raid through your MB may give you the option of having the OS in the raid.
But why would you want it? Raid 5 is not fast, it would slow down your OS, think of a page file in the raid - it is reliable.