1. the .js file is being loaded in the header because you've located the file in the jscript folder for your template. This is probably what you want, so this is okay:
HTML Code:
<script type="text/javascript" src="includes/templates/praiseandplay/jscript/jscript_praiseandplay.js"></script>
2. In your bottom centerbox you have a commented copy of the script with a big long file path that will not work on a webpage because the path is too long:
Code:
<!-- <script language="javascript" src="/kunden/homepages/19/d158832336/htdocs/praiseandplay/catalog/includes/modules/pages/main_page_js/jscript_praiseandplayscroll.js"></script> -->
It can likely be removed.
3. I decided to take a look at the js code you're using to see how it's supposed to invoke the scrolling .... only to discover that the code in the file has nothing to do with scrolling .... instead it's css-top-menu code ....