Please check this blog post for an explanation of this code: http://www.undpaul.de/blog/2013/06/14/changing-ckeditor-skins-drupals-wysiwyg

gistfile1.php

<?php

/**
  * Implements hook__wysiwyg_editor_settings_alter().
  */
function MODULENAME_wysiwyg_editor_settings_alter(&$settings, $context) {
 global $base_url;

  if ($context['profile']->editor == 'ckeditor') {
   $skins_path = drupal_get_path('module', 'MODULENAME') . '/ckeditor/skins';
   // For flexibility we use a variable to get the active skin name.
   $active_skin = variable_get('MODULENAME_skin', 'silver');
   // Set custom skin.
    $settings['skin'] = sprintf('%s,' . '%s/%s/%s/', $active_skin, $base_url, $skins_path, $active_skin);
  }
}