It appears this is possible only through code (not within the meta box builder) by specifying show_in_menu => 'edit.php?post_type=[your_custom_post_type_slug]'
Yes, that's possible only through code. The MB Custom Post Type plugin allows you to put the CPT menu in the WordPress's main menu only. I'll try to make an update to support that.
I've just updated the MB Custom Post Type on Github to support moving the CPT to be a sub-menu of another existing menu. Please try it and let me know how it goes. The new version will be available on wordpress.org soon.