I know Flynn is working hard to get this already amazing theme ready for its close-up. While I had some trouble getting new widget areas to show up properly, and then getting rid of traces of them in the widgets admin area, I also had some success on a test site.
Some background: I'm using the Sponsors Slideshow Plugin to make several instances of banner ads. Our newspaper has many advertisers who all want to be on the front page, and just about everywhere on the site. How to satisfy all of them? A slideshow is the obvious way. Before we switched to Wordpress, we used a cgi Perl script called csBanner. We are still using the code for it, hard-coded into Atahualpa's header config file, for our top-of-site banners. But I wanted to be able to have a regular widget area up there, not just in the sidebars, and now we're able to do it.
I'm taking it slowly, using a test site to try out these ideas. It's ugly now, but I need to see how it all works together: a Sponsors Slideshow widget area under the logo, and one in the right sidebar. http://www.skilovers.com/wp/ On the real site, we'll have those two as well as 2 more in the right sidebar, stacked up.
So, Flynn, keep up the great work, because you are getting really close! Once I'm sure this is all going to work, I'll switch the newspaper site from ATA 3.2 to 3.4.2 and get it all in place. Thank you for this wonderful theme.