You have two options. First puppet pin will not work on layers that have moving areas of transparency. IOW, if you animate the bird so that it appears to go into the tree, then pre-compose the crow and the tree and try to puppet pin both together you'll end up with a problem with the mesh because it is based on the opacity of the layer. When the bird moves outside the mesh created in the first frame it will leave parts behind.
Without seeing your comp with the modified properties of all layers revealed it's pretty hard to visualize exactly what is going on but I suspect that the easiest solution may be to drop a colored solid behind the animation of the bird moving into the tree then precompose all layers and animate the tree swaying using puppet pin, then use Keylight to remove the solid background and insert the background artwork you want in the scene. This is assuming you want the bird to move to the tree, then into the tree and have the tree moving throughout the entire scene.
The only other way I can see to do this is to use a distortion mesh of some kind to move the tree and everything else so you don't have problems with puppet pin mesh.
Sorry if Im not clear its been a headache.
Heres the diagram we made of how we want this to go down: http://i.imgur.com/CRFQ3Dx.jpg
I didnt link an AE file / comp or anything cause we dont have anything actually made yet. I wanted to get the technique down before I made it.
Yea I the tree's going to be swaying the entire scene (maybe even some of the nest). Is puppet pins not the way to go about this? You would think there would be some sort of puppet pin thats like "place a pin here so it appears behind OTHER LAYERS" and not just itself.
Please just drag your images and screenshots to this forum. I don't click on outside links that I don't recognize for obvious reasons. I don't think your link is working. If you are on windows just select the layers you are experimenting with, press the u key twice to reveal the modified properties and then PrintScreen and paste to this forum. It couldn't be easier. If you are on a Mac Shift + Ctrl/CMnd + 3 will take a screenshot and deliver it to the desktop. Just drag it to the forum.
Puppet pin meshes are based on the opacity of a layer. The mesh can extend beyond the edge of the alpha channel by making adjustments to the mesh. You can set one pin to move in front of another so arms can swing in front of a body on one side and behind on the other.
Have you spend some time with the help files and the community resources available when you type Puppet Pin in the search help field. It is not a tool that you can efficiently use without doing some serious study and experimentation and the help files are pretty good.
Bird, tree and background on different layers.
I would animate the bird using puppet pin, animate the tree using puppet pin, pre-compose the tree, precompose the bird, duplicate the tree pre comp and draw a mask so you can put the bird between the two copies of the tree and get it to enter the hole.
Nothing magic, just layers.
BTW, it's not that I didn't know what the link to the graphic was it's just a pain to go to it when it takes absolutely no effort to embed an image. Easier then comping and pasting a link. It also did not work on my phone.