I thnk maybe you're confused between material zones (which you might use to define the sole, boot, leg that you mentioned earlier) and the groups, which Poser needs to hang its rigging on. How did you build your model, what groups/materials have you defined, and how?

Open your original model (before AutoGroup Editor got started on it) in UVMapper - the free version will do. Then do Ctrl-G to select by group, which will give you a list of the groups, followed by Ctrl-M to select by material. Which list has the zones you want to keep in it?