Drives can be mounted in just about any confiuration you like, though I would personally stay away from mounting them upside down. IBM, Compaq, Dell, HP, PackardBell(ewww) and all the other Corporation each have or had systems with a side mounted Hard Drive at one point or another.
I'd go with Hippys suggestion, you can get a rail kit which allows you to install a drive in the 5 1/4 floppy bay which is now used for CD installations amoung other things. Make sure that you have Both drives jumpers set correctly.
Drive 0: Master/with Slave
Drive 1: Slave
other than that, always remember heat is not your computer or any of the components friend