If you've added the banner client and banner ad in rotation as well as configured your site to show banners in admin.php/preferences, then the banner should show up fine in either position.

Try using another theme such as fisubice (which comes with ravennuke) and see if your banners now show. If they do, the problem is within the theme itself. If you banners don't show up in other themes then you have a config. issue either within your banner client setup, image setup, or site preferences.