So to setup flat rate shipping and get around the issue with it using the flat rate from both categories, pasting this just before the closing </head> tag in your template should do the trick:

<script type="text/javascript" charset="utf-8">
jQuery(document).ready(function() {
FC.checkout.config.orderFlatRateShipping = 9;
FC.checkout.updateShipping(-1);
});
</script>
 
<wrap hi> This will make the shipping charges to be 9 no matter what is added to the cart. <wrap>

• http://forum.foxycart.com/comments.php?DiscussionID=4389&page=1#Item_14