I had the same problem and this is what I did.
I opened the file called 'tpl_product_info_display.php' which is located in 'includes > templates > [YOUR_TEMPLATE] > templates'. This file displays the information about your product (and it's commented very well, might I add). Inside the file you'll see the code for your "Attributes Module" (<!-- bof Attributes Module --> ... <!-- eof Attributes Module -->) and the code for your Shopping Cart box (<!--bof Add to Cart Box --> ... <!--eof Add to Cart Box -->).
Near the end of the code for the Shopping Cart Box you'll see:
<?php if ($display_qty != '' or $display_button != '') { ?>
<div id="cartAdd">
<?php
echo $display_qty;
echo $display_button;
?>
</div>
Insert the "Attribute Module" code after, <div id="cartAdd"> and your problem is solved.
The final code should look like this:
<?php if ($display_qty != '' or $display_button != '') { ?>
<div id="cartAdd">
<!--bof Attributes Module -->
<?php
if ($pr_attr->fields['total'] > 0) {
?>
<?php
/**
* display the product atributes
*/
require($template->get_template_dir('/tpl_modules_attributes.php',DIR_WS_TEMPLATE, $current_page_base,'templates'). '/tpl_modules_attributes.php'); ?>
<?php
}
?>
<!--eof Attributes Module -->
<?php
echo $display_qty;
echo $display_button;
?>
</div>



