Look at [poll module][1] for a good example of this.

You can simply (with item being something in your form);

    $form = $variables['form'];
    $variables['item'] = drupal_render($form['item']);
    $variables['rendered'] = drupal_render_children($form);

However there are other ways of achieving this and keeping the rearranging within the UI (*/admin/config/people/accounts/fields* etc) by using `hook_field_extra_fields` - [poll module][2] does this as well I've noticed.  It can be used for adding existing base fields which don't otherwise show in the Manage Display UI (like node author, created, updated times, etc) - here's an example for [user picture][3].

  [1]: https://api.drupal.org/api/drupal/modules%21poll%21poll.module/function/template_preprocess_poll_vote/7
  [2]: https://api.drupal.org/api/drupal/modules%21poll%21poll.module/function/poll_field_extra_fields/7
  [3]: http://foggyperspective.com/article/positioning-users-profile-picture-manage-display-screen