Ah, got it. I think i understand.
If you have a rigged character and you add the puppet tool – the geometry – the layer – is now at the mercy of the puppet tool. If you want to have that artwork react like it did before activating the puppet tool, you have to make a bone for the puppet pin point and attached (parent) that to the original setup. Otherwise you have to use the puppet IK technique – which is a different set-up.
Does that help?