These Hooks are called each time the AssemblyLine cycles through the connector list. If you have enabled the override Hook, only the On Error Hook is called. The GUI will give you a clue when a Hook is deactivated by an overriding Hook, by showing a message at the top of the Hook's script window.
For example, if you override the GetNext operation, the Hooks in the Iterator tab will not be called. The After <mode> hooks are always called to trap errors and success, regardless of whether the override Hook or the "normal" Hooks are called.
Also remember that when you override a mode, the attribute map for that mode is not performed. For example, using the Override GetNext Hook means that you have to populate the work entry manually.