The Characterize option creates a link between the bone or joint objects defined for your character in the Mapping List and the character engine in MotionBuilder. Since all characterized characters link to this same engine, you can create a library of characters whose animation can be interchanged.
The Characterize option also stores the stance of your character, which can act as a starting or rest pose. When creating models for use in MotionBuilder, save your biped or quadruped model in a stance. There is a separate recognized stance for each type of model. See Bipeds and quadrupeds.