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:

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.