You just have to ensure the name/value of the fields is appropriate.
For example, if the key is
my_field and values are:
All checkboxes should have a name of xthreads_my_field[] and values as shown above, such as
I just noticed an issue though: it won't show whether they're checked or not. :/
If you don't mind code edits and want to change the underlying HTML, it's in inc/xthreads/xt_updatehooks.php:
First instance is just for the "blank value". Note that it affects both checkboxes and optionbutton inputs.
I'll consider exporting this to a template in a future version.