We might be suing a different workflow.  I just used the transfer utility and it autogroups, rigs and weightmaps the object.  I couldnt locate in teh dialogue how to tell it which bones to include/omit

 

Quote - >>> I need to figure out how to tell it which bones to include... my boots dont need individually wiggly toes!!

The boots I made ONLY include Shin, Foot, and Toes group - for the groups in the models themselves. Not the individual toes, but the PARENT of all those little wigglies. So the very very very front of the boots is just the "Toes" group. 

I didn't include any of the individual toe bones when I rigged them either. Rigged up fine that way in both DS and Poser as far as I can see.