Hey Lasareath, I was looking at doing something like that just earlier today. I found this page particularily helpful:
http://green-beast.com/blog/?p=157
You would put a slightly varied version of that html/php code (no need for the rss stuff perhaps etc) in header.php just before here:
Code:
</td>
<!-- / Left Sidebar -->
just after
And then put the css stuff in ATO -> Add HTML/CSS Inserts -> CSS Inserts.
Hope that helps!