Your best bet if you want them to show using the default drag and drop function is to register a custom taxonomy for the custom post type, http://codex.wordpress.org/Function_Reference/register_taxonomy.
You can also use the taxonomies parameter when you register your CPT function.
http://codex.wordpress.org/Function_Reference/register_post_type
The alternative is to make a custom filter for your nav menu that is populated from your custom post type, though in most cases I recommend the first option.
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