There are normally two IDE channels provided by the chipset of your mainboard, the primary and the secondary channel. For one channel there is one IDE cable. You can connect two devices with one cable, so you can connect up to four devices. Two devices at one cable need a difference to be recognized properly. So you have to “jumper” them. Every device has a little jumper at its back. There are three possibilities to shorten the pins: Master (Ma), Slave (Sl) and CableSelect (CS). Every channel needs at least a Master device. So when you’re only running one device at one channel it has to be set as Master (use the end of the cable then, otherwise there could be unwanted reflections!). When you’re running two devices at one channel, one must be set to Master and the other one to Slave.
When you’re running devices in CableSelect mode, the device at the end of the cable will be set to Master, the device in the middle to Slave automatically. But this doesn’t work with every device, so it’s recommended to set the jumpers clearly!
In the history of computers the primary IDE channel was used for Harddiscs, as the computer searches for boot device at primary Master. For not “disturbing” the Harddisk, there was often no more device connected to the primary channel (one channel only has one IRQ, this was fatal in old PIO times without DMA). So only the secondary channel was left for optical devices. This is the reason why it’s recommended to run a DVD writer as secondary Master!
Nowadays there are also seperated Harddisk controllers (SATA and/or RAID), so you can use both IDE channels for optical units. Here is also recommended: Set the writers to Master when you experience a problem!
I hope, that cleared it up a bit…