How do motor6Ds affect bones and vice versa?

I am currently trying to create a skinned shark rig. While the rig works with motor6ds, I need bones in order for the shark to be skinned. My understanding is that if you have a model with both motor6ds and bones, you can use motor6ds to move the individual joints and the bones will simultaneously work to skin them. (Note, according to my understanding, this does not require any additional coding for the bones.) I’m starting to think my understanding is wrong, as using rigged meshes causes the model to go crazy.

Am I wrong? Do I need to use either bones or motor6ds to move joints?

Quick note: The working rig that solely employs motor6ds is not moved with the animation editor. Rather, a script gives the offset values for the motor6ds. I am using this CCDIK Controller.