I think you should use single_template
filter hook to load your template from a subdirectory. The full code will be like below-
function the_dramatist_get_custom_post_type_template($single_template) {
global $post;
if ($post->post_type == 'your_post_type') {
// Your post type directory with the post type template file name
$single_template = dirname( __FILE__ ) . '/post-type-template.php';
}
return $single_template;
}
add_filter( 'single_template', 'the_dramatist_get_custom_post_type_template' );
Please read the documentation for further information. Hope that helps.