sph,
Glad it worked and, yes, it's simple.
The only file included with this mod is the one for the includes/templates/CUSTOM/templates/tpl_modules_categories_tabs.php.
It contains the query
$categories_tab_query = "SELECT c.categories_id, cd.categories_name FROM ".TABLE_CATEGORIES." c, ".TABLE_CATEGORIES_DESCRIPTION . " cd WHERE c.categories_id=cd.categories_id AND c.parent_id= '0' AND cd.language_id='" . (int)$_SESSION['languages_id'] . "' AND c.categories_status='1' ORDER BY c.sort_order, cd.categories_name;";
$categories_tab = $db->Execute($categories_tab_query);
The while following the query is what populates the menu with the categories selected.
You will need to "massage" that query in order to change the selection process.
I hope you will understand that this is not a thread to discuss SEO or other items other than problems with the mod or it's installation.
Also, it could muddy the waters if we begin discussing the many ways the mod can be the basis for something way bigger and better.
The mod says Simple and I think this thread should stay simple.
Perhaps someone will PM you with a quote or you can search the Add Ons for more powerful menu mods. Perhaps when 1.5.0 is finalized, someone will make this a more powerful "select your category" option at that time.
I am not the author nor a user of the mod, but modified it to make it validate and operate as the original author intended. With that, I committed to assist with installation and operation problems. We have already seen that template choices even from Zen Cart add ons can effect the operation of this mod. Be sure that any template chosen for your site(s) follow standard Zen Cart process and validate before going further.