Hello,
You can parse the HTML output and use the parseCheckboxes method to update checkboxes by order. This doesn't require knowing information or adding bookmarks; checkboxes are updated by order.
Or you can use DOCXCustomizer to do more complex updates. For example knowing bookmark names to update specific checkboxes.
If you open a support ticket (https://www.phpdocx.com/support) we can generate a custom sample script.
Regards.