Replacing the banner with a SWF file will involve doing a little custom hacking on your part. You'll want to head to the Advanced Layout Options and download the current layout file (right click, save as). Then, on that downloaded file, edit it with a text editor, and where the current background is being shown, you'll want to add the embed code for the SWF file.

In the template you're using, look for:

<div id=background> 
	<div id=logo onClick="location.href='news.php'"></div> 
</div>