This is the part of the View Cart code that calls the box.js script to generate the cart overlay:
<script language="javascript" type="text/javascript">
<!--
function EJEJC_lc(th) { return false; }
function EJEJC_config() {
EJEJC_INITCSS = false;
}
// -->
</script>
<script src='
http://www.e-junkie.com/ecom/box.js' type='text/javascript'></script>
...so you can put that in a common WP template file or header field that would get inserted into every page. You may notice the extra EJEJC_INITCS line, which should fix the layout issue you described. Make sure you are using our standard JavaScript button code (i.e., make sure you have not unchecked the box indicated to disable JS on our Get Button Codes screens).
More WordPress tips and advice are in this other forum thread:
http://www.e-junkie.com/bb/topic/2534