in the jiggle bone panel i’ve included buttons to select all the jiggle bones in your armature, and then a bake button to bake them. the baking is just blender’s bake action operator, so you can read up on that if you want to familiarize yourself with the overall baking procedure.
as for the bones not jiggling when duplicated, my only suggestion would be to toggle the ‘enabled’ state. the add-on keeps an internal list of all bones enabled for jiggling, and unfortunately when duplicating an enabled object, it does not trigger this list to update automatically.
i really need to make a tutorial video to help with common questions about usage!