hook_wysiwyg_editor_settings_alter.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);
  }
}
?>