To set the initial value:

    $ewrapper->field_user_permission = array($user->uid);
    $ewrapper->save();

To set additional values:

    $ewrapper->field_user_permission[] = $user->uid;
    $ewrapper->save();

This method also works with wrapped multi value [Entity Reference][1] fields.


  [1]: https://drupal.org/project/entityreference