$Collection=Mage::getResourceModel('catalog/product_collection')
    ->addFinalPrice()
                        ->getSelect()
                        ->where('price_index.final_price < price_index.price');
// Get product ids
$productIds=$Collection->getAllIds();
$categoryId = 'Your Category_Ids';  /
$category = Mage::getModel('catalog/category')->setStoreId(Mage_Core_Model_App::ADMIN_STORE_ID)->load($categoryId);
//get the current products
$products = $category->getProductsPosition();

foreach ($productIds as $id){
    $products[$id] = 1;//you can put any other position number instead of 1.
}
//attach all the products to the category
$category->setPostedProducts($products);
//save the category.
$category->save();