MDD's have two drive cages for 3.5" hard drives. Each can hold two drives for a total of four, not counting the two optical drive bays.
The drive bay under the power supply use the ATA-100 connector next to the cpu heatsink. The drive bay under the optical drives use the ATA-66 connector nearest the optical drive bay fan. The optical drives use the ATA-33 connection nearest the door hinge.
The drives bays are identical and interchangeable. If you are missing the one under the optical drive cage, you can find them for sale on ebay for not too much money.