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Firstly, i would use NTFS, its more stable, more secure, and doesnt have FAT in the title. The easiest way to do it would be to connect only one drive at a time, install windows on each, then plug them both in together and see which one it boots to, which ever one that is, i would then download a boot loader suck as LILO for windows, and install it on that drive, this will enable you to choose which ever windows installation to boot into.

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