Slash I would recommend that you:
- duplicate the head
- add a live blendshape in local space from the FaceTrainer puppet to your duplicate geometry
- select the skeleton and the duplicate head and add a skinCluster
- copy the weights from the puppet head or paint your own.
- go the the zrtPlayer node and disable "skinning"
- hide the puppet geometry
- turn the blendShape on and leave it on.
At this point, if you want to add blendShape correctives, you will just need to add it before the skincluster on your duplicate head to get the result you are looking for.
I hope this helps!