To make DuplexZen work, you first need to customize the configuration file located in the same directory as the executable: PageCloner.exe.config.

This is a standard .NET XML configuration file which you may safely edit in Notepad. Make a back-up first, and be sure not to violate the XML syntax rules. You may want to look for free .NET Configuration File editors if in doubt.

These are the settings you can or need to customize:

Site:
the Site Collection base URL containing the Web Part Page to duplicate.
Default value: http://dualserver

Web:
the site-relative Web Site URL containing the Web Part Page to duplicate.
Default value: /

Folder:
the name of the Document Library containing the Web Part Page to duplicate.
Default value: Shared Documents

Extension:
the file extension of the Web Part Page to duplicate.
Default value: .aspx

ListView_ToolBar:
the default Toolbar setting to apply to cloned List View Web Parts.
Default value: Freeform. See MSDN for valid values.

ListView_Where:
the CAML to set to the View associated with List View Web Parts.
Default value should be changed or cleared.

Elevate:
Whether to SPSecurity.RunWithElevatedPrivileges, i.e. run with application pool account privileges.
Default value: True

There are other settings but you should be able to get up and running with those initially. You can also find-and-replace Web Part settings while duplicating from a source to a target Web Part Page.

Post here for any questions!

"ListView_ToolBar" can be "Standard" or "FreeForm", corresponding to:
CAML View Schema: Toolbar Element (MSDN)

"ListView_Where" is XML to specify filtering and/or sorting defaults, corresponding to: CAML Query Schema: Toolbar Element (MSDN)