I'm doing the same 3 drive setup and here's what I do:
Primary:
Master: Boot Drive
Slave: DVD-ROM
Secondary:
Master: DVD-Burner
Slave: CD-Burner
Secondary drives can be reversed as needed.
This works well if you are limited to just 2 IDE channels as for CD or DVD copying you can use the DVD-ROM as the reader and not deal with two drives fighting over the same IDE bus. For burning from the hard drive to a CD or DVD, then the same is true also. The only bottleneck will be if you read from the DVD-ROM to the hard drive, which you can avoid because you can read any disc from the other channel's drives. Does this make sense?
P.S. If you have a secondary IDE controller or are doing RAID, it's even better because you remove the possible DVD-ROM-->HD bottleneck