Jumper settings.

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RAID, or non-RAID makes no difference for the master/slave relationship. According to Apple's service manual, the bay where you install the drive determines that master/slave position, and you don't need to mess with jumpers at all. I interpret that to mean that you would install a hard drive in the drive module, then insert that drive module into whichever position that you choose. Jumper settings on the hard drive itself are ignored.
The drive installed in bay 1 will be the master drive, and should have the operating system installed on that drive.
 
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