Hmm... I'm still getting acquainted with the BIOS. I haven't figured out how to check ports in the BIOS (I'd try right now but the comp is in the middle of a download and my internet is slooowwww.
However, I did try opening the boot menu in the BIOS earlier today, and It appeared to have both hard drives in there. The reason I thought it wasn't being detected at all was that the 2nd drive does not appear in the Boot Priority section. Is there a setting that can enable it to appear there, or is it still some kind of miscommunication between the drive and the mobo?