Glad it's working, and admin control sounds like a good improvement. I think you want the top set of middlebox code below
PHP Code:
<?php } else { ?>
<h1 id="indexCategoriesHeading"><?php echo $breadcrumb->last(); ?></h1>
<?php } ?>
If it is above that, the middleboxes above the category listing can only show when the define_main_page is enabled (if ($show_welcome == true)). This change will not affect the location of the top middlebox set.
I would suggest adding a third option, to put the middleboxes below the featured etc. centerboxes (just below the while loop). If you are adding the switch anyway, you can easily make it more flexible now.