If you have an ATA66 controller, then you might see a slight speed difference in speed if you keep only ATA66 devices on the primary chanel.
Each channel chooses the fastest protocol that all devices on that channel support. CD-ROMs don't support ATA66 so you are running you hard-drive in ATA33 mode right now. The reason that I say slight is that few drives availible now use more than a 33 mb/sec transfer rate.
If you do a lot of copying of CDs from CD to CD then you will be much better served by leaving the configuration like you have it now, with the 2 CD drives on seperate channels.