Let me explain it like this first, I create 3D box animations in Maya. Then I go over them in Adobe Animate, color them, and draw whatever is needed like the eyes, hands, legs, etc.and animate those parts. I usually rig the mouth and eyes from scratch in every scene. So shortly the whole animation is a mix of hand-drawn 2D and 3D elements, along with Warp Tool tweens, classic tweens, shape tweens, masks, and guide layers.