When you have put this in the index file:
<script language="javascript" type="text/javascript" src="<?php echo $ja_template_path;?>/scripts/thenameofthefile.js"></script>
You have added the mootools script to the template, from this point its in basic up to you what you wanna do with the template? And which functions you wanna add.
I suggest to go to the mootools website(or jquery one) and download the full package unless you know which functions you allready need.
When you have your site set up the way you want you can in basic add whatever functions you need.
Btw, i just got back and online again now,so if you still need the help i promised you let me know and i can help you out with it now, sorry for the delay here.
