patch for centering the popup window:

js/popup.js:56

         var left = (screen.width - width)/2;
         var top = (screen.height - height)/2;
         win = window.open(url + '?' + params.toQueryString(), 
opts.name || uniq, 'menubar=' + menu + 
',toolbar=no,location=no,status=yes,scrollbars=yes,resizable=yes,width=' + 
width + ',height=' + height + ',left='+left+',top='+top);

Why?  This is the only location to guarantee the window has a chance 
of fitting entirely within the monitor.

You can edit the position locally to whatever you want.

js/popup.js:1744

compose window's position is hardcoded: left=0,top=0
Please position the compose windows somewhere in the middle, near the 
main browser window.