$form['folder_name'] = array(
      '#type' => 'textfield',
      '#title' => t('Folder Name'),
  );
  $form['document'] = array(
    '#type' => 'managed_file',
    '#upload_validators' => array('file_validate_extensions' => array('xml')),
    '#upload_location' => 'public://',
    '#submit' => array('custom_document_submit'),
    );
function custom_document_submit($form, &$form_state){
  $destination = $form_state['values']['folder_name'];
  $validators = array();
  $file = file_save_upload('document', $validators, 'public://'.$destination);
}