Here's a video of the two directors of boxtrolls explaining the behind the scenes of the film, including how the puppets are put together, They explain how the boxtrolls have completely removable faces and not just have a face like most do. One of the boxtrolls had about 1500 faces which allowed for 1.4 combinations for the face.
They put the Maya modelled face playblasts on top of the animatic to see if they have all the 3D faces they need to create the scenes they need.