Ok I had a bit of a problem when I tested them in Maya, because I used only the Marmot's head it said that the whole body could not be deformed by the blend shapes.
So... I had to have two versions of the Marmot, one without the body and one without the head. The blend shapes then worked on the head. And after I just combined the meshes to get one whole body... I just don't know how this will affect the rigging if at all