the filesystem shouldnt matter - Im sure Ive mirrored fat and ntfs without problem in the past. As to the partitions, you should be able to choose which partitions to mirror - so you could just mirror the system partition or choose both - if the disk you are mirroring to is the same size or larger. My recommended setup is mirrored boot drives (or partitions, but for performance drives) and raid5 for the data area
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