Restoring your Virtualized Apps when there is no way of recovering their registry settings is a difficult scenario. Here's some help.
For users (like me) who use disk cloning/imaging tools to restore a fresh C:\ disk image when problems occur, the usual problem is re-installing all those applicaions that weren't in that image.
It's nice to have your main app launch automatically as soon as you activate a layer.
I don't know what method others use, here's one that I found and seems really easy.