Let's say you have a form that you want people to fill out and then be able to edit later and in this form you have [at least] one set of checkboxes that you want to populate to a custom taxonomy.
In my case I have a Custom Post of "Students" that had two custom taxonomies attached to it; "Teachers" and "Classes." I needed people to be able to edit a "Student" entry and change what teacher and class the student was in.
Here's what I did...
Use this multiple times on one form. Just duplicate it as needed.
Make sure you click the "Show Values" box on the checkbox field in the admin as you're setting up your form. The "Value" should match the slug name from the taxonomy.
Hope this helps!