I've added custom widgets to the top and bottom of the center area using one of the provided codes. When I go to the Widget section of the WP admin, they aren't there. Using WP 3.7.1 and ATA 3.7.12. Any thoughts?

Did you view the front page of your site before going to the widget page. That way the code that builds teh widget area wll be executed.

That did it, thanks!