Have you tried to set the location rule to Taxonomy Term and select your custom taxonomy?
This will add your field to all your terms in selected taxonomy.
It sounds like everything is working, but you are just using the wrong code to display it in the front.
Try using something like:
Locations: <?php echo implode( ', ', get_field( 'field_name' ) ); ?>
Take a look at the documentation for Checkbox here: http://www.advancedcustomfields.com/resources/checkbox/
look under Displaying multiple values
Try with 'orderby' => 'meta_value_num'
I think you can remove 'type' => 'NUMERIC'
See more here
