When connecting to IDE drives (whether they be hard disk drives or optical drives) on the same cable, the computer needs to be able to tell them apart. When using a 40 wire IDE cable, you have to identify one drive as Master and the other as Slave. You do this by positioning the jumpers on the end of the drive according to the diagram on the drive itself.
When using an 80 wire cable, set the jumpers on both drives to the 'cable select' position and their Master and Slave classifications will be determined by their position on the cable.