so as to fasten sheets together when they come thick, to avoid loose-leaf falls apart. If the thickness of documents is less than half inch, you may try to use a binder clip instead.
When you do punch holes, punch 2 holes on top of documents. Then you may want to take a look at Fastener also.
Flags may help you too, to separate documents.
Binder Clips
Fasteners
Flags
In case you don't need to use a punch that often