There's a new document up on twocanoes software's website: http://twocanoes.com/support/winclone/using-jamf-casper-suite-and-winclone-pro-to-image-a-lab-of-dual-boot-macs "Using JAMF Casper Suite and Winclone Pro to Image a Lab of Dual-Boot Macs"
You need to use Winclone version 3.4 or later for the best results with JAMF software because the Recovery HD renumbers the BSD partitions after installing OS X.