You can get mounting adapters for putting hard drives in the 5 1/4 bays. Sitting it on top of the cd-rom drive is not real smart. A bump on the case would send it flying around in the case. Not a good thing.
Besides the metal frame is part of the heat disapation system on the hard drive. Sitting it on top of something else trying to get rid of heat and things tend to over heat. The brackets I'm talking about can be had at just about any place that sells computer parts. Run about 3 or 4 dollars.