For on-the-fly copying of CDs, best way for your drives to be configured would be:
Primary IDE channel
Slave: cd-rom drive
Secondary IDE channel
Master: DVD burner
If your cd-rom drive is currently the slave on the secondary channel, you won't need to adjust any jumper settings at the rear of any of the drives. Also make sure you've got an 80-pin IDE cable for both channels to get best transfer rates.
I have a DVR-108 (master) and a DVD-ROM drive (slave) on my secondary channel and get UDMA mode 5 for the burner and 4 for the DVD-ROM. Mine is configured this way because I don't trust on-the-fly transfers.