Why use your biggest disk as your primary? Charlie Kindel explains it 4 or 5 posts down in
this thread, but basically its due to the way the beta is managing the storage pool.
As for adding your array as individual disks, no there won't be a problem. That's Microsoft's recommended configuration, as a matter of fact. "RAID is not a supported configuration" to quote several folks on the development team. And I understand why they say that; RAID is not nearly as easy to set up as just plugging in another disk.