Check out detailed breakdowns below for a lot of the shows I worked on to see how stop motion animation is very similar to live action VFX. Practical puppets and decorations are shot on stage. Some times (which nowadays almost equals to all the time) blue or green screens are used to block out part of the set for the future set extension. Or card might be dropped back behind one of the puppets to help with upcoming extraction. Footage from stages would be delivered to VFX where in a very similar to live action VFX manner it will be processed, tracked, keyed, augmented with beauty and compositing work to be delivered as a final shot that will be used in the film.