Study anatomy books to learn the anatomy of humans and animals. By understanding internal bone structures, you will know how creatures, real or imagined, will move in your stop-motion animation.
Sketch preliminary drawings of puppets on a sketchpad with a pencil. Think about the topic of your film or video, and which colors you wish to use.
Sculpt a model of your puppet sketches from polymer clay. Make these in three dimension, which means you must look at all sides of the puppet. Stand the sculpted model on your puppet set to see whether or not it works. You might need to go back to the drawing board and rethink your design, or you might need only a few minor changes.
Create additional puppets and extra body parts in exactly the same fashion as your final puppet. For stop-motion animation, pose your puppet and move it for each frame. Having extra heads with different expressions, or additional puppets already complete before you start shooting is better than having to sculpt during production.
Stand your puppet in your puppet set. Shoot your puppet according to your script, moving different body parts slowly for each frame.