I figured out myself how to do this. It's just template overriding.
Just add a folder in your hmtl template folder called "jw_disqus".
Copy the /plugins/content/jw_disqus/tmpl/article.php file there and add the following lines after <?php echo $row->text; ?> :
<div id="bottom_art">
<?php
$document = &JFactory::getDocument();
$renderer = $document->loadRenderer( 'modules' );
$options = array( 'style' => 'raw' );
echo $renderer->render( 'bottom_art', $options, null);
?>
</div>
You'll make a new module position at the end of the article just before disqus.
Hope it's useful for someone.
