When you have two devices on the same cable, they can not work at same time.
Let say that we copy files from a CD to the hard drive. If the CD is on a same Channel (i.e. slave on the HD cable), the constant alternation between the two will slow the whole process. If the CD is on another channel the CD and the HD can work in tandem, and the process will be faster. In other word the way you connect them depends on they you work.
The best is to use a Mobo that have four IDE channels (like the Abit BE6), or to add a pci ATA66 (100) card, and to use the ATA66 (100) channels for the HD, and the regular IDE channels for the variety of CD, and other ATAPI devices.