There is only one cable per IDE controller. So, the two cables are for different IDE controllers. Usually the older 40wire type is for the CD Drive, and the 80wire is for the HD which is more sensitive to cable quality.
Using both a Master and Slave halves the bandwidth to each drive, so unless you REALLY REALLY need another drive in there (and don't have a PCI IDE/SATA controller), it's better to have only one drive on the HDs bus.
A note about the cable:
If cable select is chosen on the drive, the layout of the connectors on 40wire cable is:
motherboard ==== Master ==== Slave
-If you're not using the Slave connector, it's possible to snip off that cable segment.
On the newer 80wire cable, it is:
motherboard ==== Slave ==== Master
-You shouldn't snip off a segment of this cable.
For Maxtor drives, it's better to use the "Single Drive setting," for any drive it's better to choose the "Master" or "Single Drive" setting, not cable select if there is only one drive on the bus.
the extra 40wires in 80pin cable are ground cable to reduce crosstalk among the 40pin cables.