I have heard that when copying CD to CD on the fly, having them on the same channel doesn't work. but since A. I don't do that, and B. I think it looks cleaner in the case when the drives are seperated (CD's and HD's) I don't care...
my DVD-ROM and my burner are on the same channel, as my 2 hdd's are on the same channel. all is fine, CD burner works perfect and so does DVD playback/reading CD's.