I hope this helps, but I have to make a few corrections to the previous post. Please don't get mad at me.
1) It doesn't matter which end of the cable the master is on for IDE drives.
2) If the jumpers were conflicting (IE both set as master) it would not boot at all. However, as stated by vududoc you do want the boot drive as master.
3) Yes, sometimes having both cd drives on the same channel can cause problems, but unless that is the problem you want the cd's separate from the hd's. The reason is, with IDE the channel is only as fast as the slowest drive, so the cd's will lower the transfer rate of the hd's if you have a cd drive paired with the hd. As an example I have 2 hd's on my primary channel (120gb and 80 gb) and a dvd-rom and a dvd-rw on the secondary channel.
4) If the newer drive is a newer standard than your IDE controller that can cause issues. Such as if your controller and/or IDE cable is only an ATA-66 and the new drive is a ATA-133.
Also, if the OS is on the slave drive it will boot slower because it will be looking for the OS on the master first. It may also check the floppy and/or the cd drives before the other hard drive. It depends on how the boot sequence is setup in the BIOS.
Finally, vududoc, could you explain what you mean by "You may find it easier to assign the second CD as a "detatchable temporary device" using your USB port." I have no clue what you mean there. Thanks, hope this helps.