RAID cards can handle multiple arrays, but not all will do what you want. The Apple RAID Pro card will not. You need a card that will function under both OS X and windows via boot camp.
The reason is that the OS X can't manage an array for windows, and vice versa. So the controller must be able to operate under both OS's.
Such controllers do exist, but aren't cheap. Since the Apple RAID Pro goes for $800, you can find cards that work for this amount or less.