If you really want separate hard drives you can buy a hard drive cage. They fit in a 5.25'' bay. Of course, you'd probably want two of them because it'd be a pain to remove one hard drive out of the cage and put in a second one.
But, you might be able to get away with keeping your Primary o/s hard drive inside your case and use the cage for your 2nd o/s by editing the boot.ini file. Anyone else wanna confirm this?