I'm going to assume the obvious point that you have a SATA capable motherboard or at least you have a SATA controller card. If so then yes you can pick whichever drive you want to boot from, depending on how old the motherboard is and how they have implemented SATA you might need to install SATA drivers but this is quite rare now.
For ease I would suggest that you disconnect all other drives apart from the one you wish to install Windows on to, simply because Windows can occasionally choose to put some important boot files on the first drive it comes to, which is normally an IDE/ATA drive, regardless of what you are actually telling it to do.
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