Nope, I mean the actual root of the entire site (/). The same directory that is holding the web.config file for your mojoPortal site. I used the following:
<script type="text/javascript" src="/js/jquery.easing.1.1.js"></script>
<script type="text/javascript" src="/js/jquery.jcarousellite.js"></script>
And by the structure of your skin, I doubt your mojoPortal installation is in a sub-directory or virtual directory of any kind so the above should work for you.
Thanks,
Joe D.