It depends on the speeds of your hard drives really,at the present most CDs tend to run at a slower speed than harddrives,up to 33Mb/s so having on the same IDE as the harddrive will slow it access/read times down if it is a fairly fast drive i.e UDMA 66 or 100 [66-100Mb/s].Some modern boards are designed with the main IDE0 as a faster port for the drives and IDE1 for CD/DVD etc.
Personnally if the drives are the same speed I`d but them on the same cable and the CDs on the other,but you may hit problems with copying CD to CDRW this way and have to copy to drive first.
I`m sure some of the more knowlegable techs here will give you more insite but heres my four farthings worth