How to: add option to add more checkboxes on custom post type

Your question is very abstract. As far I understood you want some thing like categories.enter image description here

So for that adding metaboxes is not necessary. I think categories are enough. If categories are not full filling your need then make another custom taxonomy with 'hierarchical' => true,. I think it will serve your need. Also giving permissions to author to create dynamic meta box is not a good idea. So first try with category otherwise custom taxonomy. “Author can create dynamic meta boxes” is your last option.

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