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Ideally, you want an airflow that covers your whole case (5 1/2" drives don't matter). What you'll find in most cases (tee hee, unavoidable pun) is a few fans in the front, a CPU fan, and the power supply. This really isn't a bad setup, as it'll pull air over your hard drives, up past your video card and CPU, then out the back through the PSU. The direction doesn't really matter (front to back or back to front, whatever works best for you) just make sure that you keep it flowing.
Also, even with a good path for the air, your drive may simply be too warm. Look at getting a HD cooler, which is usually two fans designed to mount in a 3 1/2" bay and blow air directly on the drive. They should help to dissipate heat from the drive, which can then be carried away in the overall case airflow.
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