The Website Copy utility can be run in command line mode that offers a way to script the copy process and avoid having to manually interact with the wizard.

Example usage:

Websitecopy.exe /sourceConnectionString:"ServiceUri=http://crm.contoso.com/adxstudio; Domain=contoso; Username=adxstudio; Password=******;" /sourceWebsiteName:"Basic Portal" /targetFile:C:\Temp\BasicPortal.xml /targetWebsiteName:"Basic Portal" /includeSubscribers:true

Detailed list of all parameters:

/help
  Show the usage message.

/sourceConnectionString:<connection>
  A url to the CRM to contact for websites to be copied from.
  For more information regarding the connection string format please refer to the following article

/sourceFile:<path>
  The file path and name for the website backup XML to be imported.

/sourceWebsiteName:<name>
  The name of the website to be copied.

/targetConnectionString:<connection>
  A url to the CRM to copy a website to.
  For more information regarding the connection string format please refer to the following article

/targetFile:<path>
  The path and name of the file for the website to be saved to.

/targetWebsiteName:<name>
  The name of the website.

/createSubscriberRelationships:<boolean> (Default value is false)
  A Boolean (true or false) that determines if the copied website is to be set as a subscriber or child website of the original website.  This parameter is only valid if both the source and destination are CRM servers.

/includeSubscribers:<boolean> (Default value is false)
  A Boolean (true or false) that determines if the child subscriber websites should be included when the parent website is  copied either during an import from a backup file or during an export to a backup file.