I've been curious about the //, but I've been under the "if it aint broke, don't fix it" mindset. 
We got the sideboxes working on the appropriate pages with the following:
PHP Code:
<?php
/**
* blank sidebox - allows a blank sidebox to be added to your site
*
* @package templateSystem
* @copyright 2007 Kuroi Web Design
* @copyright Portions Copyright 2003-2007 Zen Cart Development Team
* @license http://www.zen-cart.com/license/2_0.txt GNU Public License V2.0
* @version $Id: blank_sidebox.php 2007-05-26 kuroi $
*/
// test if box should display
$show_blank_sidebox = true;
if ($current_page_base == 'index' and $cPath == '' ) {
$show_blank_sidebox = false;
}
else if($current_page_base == 'index' and $cPath != '' )
{
$show_blank_sidebox = true;
}
if ($show_blank_sidebox == true and $current_page_base='index' and $cPath != '') {
require($template->get_template_dir('tpl_blank_sidebox.php',DIR_WS_TEMPLATE, $current_page_base,'sideboxes'). '/tpl_blank_sidebox.php');
//$title = BOX_HEADING_BLANK_SIDEBOX;
$title='Category Option';
$title_link = false;
require($template->get_template_dir($column_box_default, DIR_WS_TEMPLATE, $current_page_base,'common') . '/' . $column_box_default);
}
?>
Thanks for your help, as always, and if I find I need to figure out the reason for the // in the url, I'll post that in a separate thread.