I have done this with templates a number of time. You need to make sure that your template is a php file (ie template.dwt.php)
you can then wrap the area you want hidden in a 'show region' under security assist
It will place code at the top of the page though,that may not be propogated to your pages that already have php above the head.
<?php require_once( "../WA_SecurityAssist/Helper_PHP.php" ); ?>
not a problem tho, as you can manually add it.