When I redid Foodizu a few months ago, I added canonical URLs to each page. The easiest to do this was with a quick PHP function:

<?php
function canonical_link(){
   $url = 'http';
   if ($_SERVER["HTTPS"] == "on") {$url .= "s";}
   $url .= "://";
   if ($_SERVER["SERVER_PORT"] != "80") {
      $url .= $_SERVER["SERVER_NAME"].":".$_SERVER["SERVER_PORT"];
   } else {
      $url .= $_SERVER["SERVER_NAME"];
   }
   if( isset($_SERVER['REQUEST_URI']) ){
      $url = $url . $_SERVER['REQUEST_URI'];
   }
   if($url){
      echo '
<link rel="canonical" href="'.$url.'" />'."\n";
   }
}
?>

to call this function you simply add in your header somewhere:

<?php canonical_link(); ?>

and it will display the canonical URL.