You can have the scriptaculous use a variable you establish outside of it's library, and use php to set that variable within the javascript
var MyX='<?PHP echo $myX; ?>';
var MyY='<?PHP echo $myY; ?>';
<script type="text/javascript" Language="Javascript" src="scriptaculous.js">
and withing the scriptaculous, find where they set those variables, and set t hem to MyX, MyY