With Windows on the primary drive and as the default OS you would want the spare drive if you plan on wiping or replacing the primary at some point. This is rather a question for the operating systems, Computer memory and hard drives, or Desktop Computers section but the answer is a quick one here.
Once Windows was reinstalled on a now clean drive or a new installation goes on a new one you would have fun copying files back from the Linux OSed drive unless you are familiar with how to a live Linux distro like Knoppix or ubuntu live for cd that will access any type of partition for file copying once you boot from the cd. Knoppix and others will show all drives installed on the system as desktop top icons. You open two of those like you would explorer windows for copy+paste but without the right click option there.
