You need to pre-compose all of the elements you want to puppet, then apply puppet pin to the pre-comp. Puppet pin works by applying a mesh to the first frame and then distorting the first frame. This means if you move elements in the frame after the first frame that the mesh does not know where they have moved and you end up with odd looking results.
Thanks Rick, but isn't this essentially the same as having both layers (the branch and trunk layers) already merged in Photoshop before importing...then trying to puppet deform the whole mesh in AE? IOW: Does pre-comping in AE afford any more flexibility (as far as being able to animate each area of the artwork independently) than importing both objects as one layer in the first place? I've been testing and I don't think so.
If it's all one mesh then, when I want to pull the branch away from the trunk, it will stretch part of the trunk (where the leaves of the branch overlap the trunk). Sorry, I should have explained that I have some overlapping in the artwork. That's part of the reason I need to have separate layers.
Here is an image of the tree with an arrow to the overlapping:
So are you saying, Rick, that I'm trying to do two contradictory things and this is impossible? (Can't deform with the puppet tool and maintain a parenting relationship at the same time?)
That's my basic question: Is there any way to use the puppet tool on two different layers while 'locking' those layers together so that their relative position doesn't change? (ie; The 'child' layer follows the moving position of the 'parent' layer.)?
That's exactly what I'm saying. You cannot move a layer that has puppet pin applied without breaking the puppet pin animation because the mesh is based on the comp frame and the first frame of the layer. Puppet pin is not based on the layer size, shape, or content. Move the layer in the comp and puppet pin breaks. Simply parenting won't cause a problem but as soon as you move one of the layers the mesh falls apart because the mesh is moving pixels that are not there any more.
Your workflow would be to put the part of the tree that is behind the trunk on a separate layer, animate the back with puppet pin, then pre-compose the front and back layers and use puppet pin to move the rest of the tree. Then you can use that comp as a nested comp in your main composition to position the tree in the scene.
Take a look at this puppet pin tutorial by my good friend Angie Taylor. You'll see how she animates a dancing bottle. Notice that the comp she is using to animate the dancing bottle is just enough larger than the bottle to allow room for the dancing. This little comp is then placed or nested in another comp to produce the final product. I would do the same with your project. Create your tree in a comp that is just larger than your tree so you can animate the movement, then nest your moving tree in another comp to do the rest of the movement.