This stuff is in the head
---------------------------

 <script type="text/javascript">
                      var need_leave_popup=false;
                      var clicked_link=false;               
                      var message = 'You may have unpaid items in your shopping cart. You must complete the checkout process for a seat to be reserved for you.';
                  
                      window.onbeforeunload = function (evt) {                       
                        if(need_leave_popup==true || clicked_link==false){
                           /*if (typeof evt == 'undefined')
                              evt = window.event;                  
                           if (evt)
                              evt.returnValue = message; */
                        return message;
                        }
                
                      need_leave_popup=false;
                      clicked_link=false;
                      //return message;
                
                }
                </script>




This is at the bottom, right before the end of body
----------------------------------------------------
<script type="text/javascript">   
                                      var k;                             
              if (Drupal.jsEnabled) {$(document).ready(function () {
                  <?php print $block['javascript'];?>
               } ) };            
        </script>
        <script type="text/javascript">
              var anchors = document.getElementsByTagName("a");              
              for(var i = 0;i < anchors.length; i++){                       
                  var anchor = anchors[i];                  
                  if((anchor.href.indexOf("localhost")==-1) || (anchor.href.indexOf("/logout")>-1)){                     
                     anchor.onclick = function(){clicked_link=true;need_leave_popup=true;};                
                  }                  
                  else
                     anchor.onclick = function(){clicked_link=true;}; 
               } 
        </script>