I tend to prefer the two hard drives to be on the primary IDE channel and the CD and DVD drives on the secondary IDE channel.
It shouldnt really matter too much how they are set up though, as long as the jumpers and the cables are set correctly.
The end connector on the IDE ribbon cable should connect to the master drive whether its a hard drive or a CD/DVD drive.
The middle connector goes to the slave.
I think the boot drive is better being set as the master on the primary IDE but if you have set a dual boot system up they seem to work ok with the second OS on either the primary slave or as master or slave on the secondary IDE channel so I suppose it doesnt matter too much which way round they are.
It just seems more logical to have the OS on the master on the primary channel