I had a hell of a time trying to figure out how to call phpBay from a theme file rather than by using the shortcode.  After sending a quick email over to the developer, he eventually gave me this code which works like a charm:

<!-- start of ebay-->
<!--?php                   $text='[phpbay]"", "", "", ""[/phpbay]';                 echo phpBayPro($text) . "";                  ?-->
<!-- end of ebay -->

I hope this helps anyone else who is trying to figure this out.