Setting up two RAID arrays on Asus P8-Z68 Delux Gen3

That's a lot of storage ,I agree that with a raid you get better speed and to have the OS on a raid would be great performance wise but I don't see the benefit of the storage being in raid. I would want a secure stable setup for things that I want to store and I don't consider a raid to be that, That's just my opinion and what I would do with my computer, in your case since it's your computer you are certianly entitled to do what you want.
I do think that even if it not neccessary I would go with a controller card for the raid 10 setup and the reason is that the seperate card may be more secure and come with software that can enhance the use and stability of the raid 10. It might be a little more expensive to do it that way but I think it would be worth it.

Thanks for the reply. I have external back up and plan to use the RAID 10 as a media server. I guess my question is more about the motherboard being able to recognize two arrays.

I'm not sure that it can , I think it's just one and you have the choice of which version.