Had a quick look againtoday and it doesn't seem to have changed. Have you updated/ uploaded all the css files?
About your second question, your featured post comes in a div at the base of the page and doesn't have anything in the css about specific positioning other than float left, which means that, yes, this is in the php code.
Unfortunately, as I can't see the php from the source, I can't advise on how to move it.
You could try looking for something like
<?php
echo "<div id='home_featured'><h3>Featured Post</h3>";
echo "<div class="feat_content">
and finished by
</div>
</div>
?>
That will give you an idea of the code block, which you can then move up in the page to just after the header (or <?php include('header.php');?> ).