but why? The second drive, being the slave, does it just leech off of the first one's OS files? What if I had a separate IDE cable for the second drive, then do the jumper pins dictate the situation at this point?
Since the computer boots off of themaster disk, and Windows is what it booted, you can think of Windows as being in the driver seat. Everything else is being controlled by Windows.
It doesn't matter if the drives are on the same cable, or in different sockets. The computer will boot from C: drive, which will be the computer set as master in the first socket.