Cable select should always be used if it's present. The drive at the end of the cable should be the master and the other one should be the slave according to best practice and convention. Therefore, no matter if there's one or two drives on the cable, cable select is the preferred configuration. If you're only hooking up one drive, just put it on the end of the cable and leave the middle connector blank. The presence of a slave drive is checked for using pin #39 and then master/slave assignments are made based on a signal carried on pin #29.
The purpose of Master and Slave is to decide which one takes precedence in the event of I/O operations taking place on both drives at the same time. It is for this reason that you shouldn't put two drives that will often exchange data on the same IDE cable, nor should you put a hard disk and an cd burner on the same cable if it is likely that the cd burner will be drawing it's data from that same hard drive. It creates a bottleneck and can lead to longer transfers in the first case and buffer under-runs in the latter.