You can put hard drives in the CD or "external" drive bays. If they're 5.25" bays you can get adapter rails that let you mount a 3.5" drive in them. The biggest difference between an "external" drive bay and an "internal" one is that the "external" bays are located behind a punch-out panel that lets you mount something like a CD or tape drive so that it's front panel is accessible. If you're using the bay for a hard drive then just don't bother punching out the panel.
Try to keep a bit of distance between hard drives (ie, leave every other bay empty) to prevent too much heat build-up.