The Winclone folder (and any contents) will be copied to the root of the Boot Camp partition after the package is installed and the image is restored. The unattend.xml will be copied to C:\Windows\Panther\Unattend\unattend.xml based on options specified when creating the package in Winclone Pro. 

The Winclone folder also contains a logon.bat script that is run at first logon if that option is selected in Winclone. Note that the script does not do anything by default by contains commented out lines to get you started.

Windows must be Sysprep'ed for the unattend.xml to be used and the logon.bat script to be run.

A common use for the Windows folder is to put the Boot Camp drivers in the folder and run the installer from the logon.bat.