Actually Manny doesn't have bones except hands and wrists and of course head and neck
Everything is combined together. The skeleton seen in the video is only an animation skeleton from 3ds max that moves a model.
The original Manny from game was too simple, to angular so i.e. moving arms was causing a major mesh distortion after combining all parts together (every part was separated - shoe, leg, hip, arm, forearm etc.). I decided to make it more round, make the mesh more complicated so all moves will be more subtle and natural.
This is my first animation in 3ds max, I choose this program because I like the way how bones behave, interact with each other. You can literally model the skeleton like a puppet or a doll, grab the hand and move it up or down and the other bones will follow.
The problems I had with animation were more connected with the mesh. I had to edit the shape of animation bones to fit exactly to the objects mesh. Beacause when its done wrong some parts of model stay in the same place, albeit the other part moves.