[Plugin: Custom Content Type Manager]Custom fields should be grouped into boxes

You can do this via CSS already — each field has its own unique ID, so fire away. It’d be poor design in my opinion to try to add a GUI to control stuff that is more easily controlled via CSS. Use the add_editor_style() function inside your theme’s functions.php.

You can also customize the HTML used to generate each field: https://code.google.com/p/wordpress-custom-content-type-manager/wiki/CustomizingManagerHTML