Calling Custom Post Meta

you can use <?=$website_url?> in the portfolio template like

<strong>URL: </strong><a href="https://wordpress.stackexchange.com/questions/32957/<?=$website_url?>"><?=$website_url?></a>

to make it like follow

<?php
/*
Template Name: Portfolio
*/
?>
<?php get_header(); ?>
    <div id="content">
    <?php 
        $loop = new WP_Query(array('post_type' => 'portfolio', 'posts_per_page' => 10)); 
    ?>
    <?php while ( $loop->have_posts() ) : $loop->the_post(); ?>
    <?php   
        $custom = get_post_custom($post->ID);
        $screenshot_url = $custom["screenshot_url"][0];
        $website_url = $custom["website_url"][0];
    ?>
        <div id="portfolio-item">
        <h1><?php the_title(); ?></h1>
        <a href="https://wordpress.stackexchange.com/questions/32957/<?=$website_url?>"><?php the_post_thumbnail(); ?> </a>
        <strong>URL: </strong><a href="https://wordpress.stackexchange.com/questions/32957/<?=$website_url?>"><?=$website_url?></a>
        <?php the_content(); ?>
    </div>
        <?php endwhile; ?>  
        </div><!-- #content -->
<?php get_footer(); ?>

You can change the placement to match your standers