I have been struggling with this same problem and found little help
with using prepare().  I will share my solution although I am still
hoping that a more efficient method exists.  I am using version 0.95

In my custom manipulator.save() -------------------------------
temp = form_fields(..all the none checkbox fields..)
temp.save()
for n in range(1, my_model.objects.count()):
      if new_data.has_key('checkbox_fieldname'+str(n)):
           temp.checkbox_fieldname.add(my_model.objects.get(pk=n))

I have tested this only for an addmanipulator, but it works.  Hopes
this helps


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