Drupal - user registration form- theming
Look at poll module 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 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.