I would experiment with placing these in the nav section of the tpl_header-php file:
Code:
<script type='text/javascript'>//HV Menu v5.411- by Ger Versluis (http://www.burmees.nl/)//Submitted to Dynamic Drive (http://www.dynamicdrive.com)//Visit http://www.dynamicdrive.com for this script and morefunction Go(){return}</script>
<script type='text/javascript' src='exmplmenu_var.js'></script>
<script type='text/javascript' src='menu_com.js'></script>
You can later move the nav section around as desired once you get the menus functioning as designed.
I do not have an install infront of me now but I recall that there is a location for js items, you should place them in this locale and you would have to adjust the src call to point to this location
Use the override system