I've been procrastinating on my problem due to being busy with work and school; now that I'm on spring break I'm going to try and fix it.
open the start menu
right click computer
click manage
under the storage bar in the left side of the window there's disk management, click that.
you should see your harddrive there and it should be completely free space unless you've partitioned it already (or unless i'm dumb)
go ahead and create a partition on that free space, windows should let you do it.
This makes it show up in Windows, but this doesn't really help my intention; I'm still getting the same issue when I add it to the RAID.
Depending on the order I add the two drives, it'll either say "BOOTMGR missing" or something along the lines of "Invalid boot device, insert proper boot media into selected device, and press any key"
I've replaced a hard drive in my raid before, I just popped it in, made the array, marked it for rebuild, and everything worked fine. I'm doing the same thing this time and it doesn't work.