mat. here is an attempt to explain it for you.
If you are putting two hard drives on the same cable/channel on the motherboard, then one of them needs to be a master and the other a slave drive. The one you are booting off of needs to be the master. The way that IDE controllers work is that you can have 2 devices on each channel. Most motherboards have 2 channels built on the motherboard. You can combine different types of ide devices on each channel, hard drives,cd-rom drives, cd writers or zip drives. On each of these devices there are jumpers, they are pretty much switches that make them either master or slave devices. There is also a way to connect both devices on a channel, and that is called cable select. Ide cables have either 2 or 3 connectors on it, one for the motherboard then either 1 for the a device, or 2 for 2 devices. In cable select mode both devices have to have the cable select switch enabled and the last drive on the ide cable is considered the master.