canonical yapıya donusturmeniz icin biraz php bilginiz olması gerekmektedir. aslında ucretsiz yardımı olmaz kolay degildir. ama ben size buraya bir vqmod birakayım.burdaki islemleri tek tek yapabilirseniz sorununuz cozulecektir.

<file name="catalog/model/catalog/product.php">
        <operation>
            <search position="before" offset="1"><![CDATA[    public function getTotalProductSpecials() {]]></search>
            <add><![CDATA[
       public function getCategoryPath($product_id) {
          $query = $this->db->query("SELECT category_id AS catid FROM " . DB_PREFIX . "category WHERE category_id IN (SELECT category_id FROM " . DB_PREFIX . "product_to_category WHERE product_id = '" . (int)$product_id . "' ) ORDER BY sort_order asc LIMIT 1");
          
          if(array_key_exists('catid', $query->row)) {
             $path = array();
             $path[0] = $query->row['catid'];
             
             $query = $this->db->query("SELECT parent_id AS pid FROM " . DB_PREFIX . "category WHERE category_id = '" . (int)$path[0] . "'");
             $parent = $query->row['pid'];
             
             $p = 1;
             while($parent>0){
                $path[$p] = $parent;
                
                $query = $this->db->query("SELECT parent_id AS pid FROM " . DB_PREFIX . "category WHERE category_id = '" . (int)$parent . "'");
                $parent = $query->row['pid'];
                $p++;
             }
          
             $path = array_reverse($path);
             
             $fullpath = '';
             
             foreach($path as $val){
                $fullpath .= '_'.$val;
             }
          
             return ltrim($fullpath, '_');
          }else{
             return '0';
          }
       }
       ]]></add>
        </operation>
    </file>    
    <file name="catalog/model/catalog/category.php">
        <operation>
            <search position="before" offset="1"><![CDATA[    public function getTotalCategoriesByCategoryId($parent_id = 0) {]]></search>
            <add><![CDATA[
            public function getCategoryPath($category_id){
        $path = '';
        $category = $this->db->query("SELECT * FROM " . DB_PREFIX . "category c WHERE c.category_id = " .(int)($category_id));
        if($category->row['parent_id'] != 0){
                $path .= $this->getCategoryPath($category->row['parent_id']) . '_';
        }
        $path .= $category->row['category_id'];
        return $path;
        }
]]></add>
        </operation>
    </file>    
    <file name="catalog/controller/product/product.php">
        <operation>
            <search position="replace"><![CDATA[$this->document->addLink($this->url->link('product/product', 'product_id=' . $this->request->get['product_id']), 'canonical');]]></search>
            <add><![CDATA[if($this->model_catalog_product->getCategoryPath($this->request->get['product_id'])!='0'){
                 $this->document->addLink($this->url->link('product/product', 'path=' . $this->model_catalog_product->getCategoryPath($this->request->get['product_id']) . '&product_id=' . $this->request->get['product_id']), 'canonical');
                 }
                 else{
                    $this->document->addLink($this->url->link('product/product', 'product_id=' . $this->request->get['product_id']), 'canonical');
                     }]]></add>
        </operation>
    </file>
    <file name="catalog/controller/product/category.php">
        <operation>
            <search position="replace" offset="8"><![CDATA[// http://googlewebmastercentral.blogspot.com/2011/09/pagination-with-relnext-and-relprev.html]]></search>
            <add><![CDATA[
             $this->document->addLink($this->url->link('product/category', 'path=' . $this->model_catalog_category->getCategoryPath($category_id)), 'canonical');
             
            ]]></add>
        </operation>
    </file>  
    <file name="catalog/controller/common/home.php">
        <operation>
            <search position="after"><![CDATA[
           $this->document->setDescription($this->config->get('config_meta_description'));
            ]]></search>
            <add><![CDATA[
        $this->document->addLink( $this->url->link('common/home') , 'canonical');
            ]]></add>
        </operation>
    </file>
    <file name="system/library/response.php">
        <operation>
                <search position="after"><![CDATA[
                    public function output() {
                ]]></search>
                <add><![CDATA[
                    if (!defined('HTTP_CATALOG')) $this->output = str_replace('index.php?route=common/home', '', $this->output);
                ]]></add>
        </operation>
    </file>