You can indeed maintain Snapshots of your Reference VM, however this will require you to use the Warm Capture method for capturing your images. This involves creating a basic SmartDeploy ISO to mount to the virtual machine to boot into the SmartPE environment. From there you can mount a network drive and use the Capture Wizard to capture and save your image over the network to your SmartDeploy Console host.
Please see the Warm Capture article for detailed step-by-step instructions:
Capture an Image from a Running Virtual Machine - Warm Capture : Support Center (smartdeploy.com)
