Separating the OS partition from the data was more relevant for NT4.0 than W2K. W2K operates best if it's all one drive. Since you're using a RAID controller, it doesn't really matter the OS will see it as a physical disk. Remember that the rule of not installing the OS on a RAID 5 partition only applies to software RAID, not hardware. Since you lose the equivalent of one HDD for parity, I recommend making a single RAID 5 logical drive using the maximum number of disks you can, and define one disk as a hot spare. That will allow you to lose two HDDs (not at the same time) and still have access to your data.
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