I just put up my first Atahualpa themed blog today and I have tried no less than 7 adsense plugins. Nothing ever shows up..no ads at all, not even any empty boxes. As an aside, neither can I get Amazon ads to show up in the sidebar widgets. I copied their product link code and paste into the widget but they stay blank. Going to tackle that later.
So I installed your recommended plugin the Advertising Manager, and again, nothing. I put in the code in the setup and everything looks good inside the plugin settings. Am I supposed to put code into the html somewhere too? I only use plugins on my other sites, which do not use the Atahualpa theme. I really love this theme, but I can't get it to show any ads. Can you shed any light on what is the problem?

I am using WP Google Ad Manager Plugin obviously with Goolge Ad Manager, or whatever Google has renamed it. It works very well at serving ads in the sidebars. Where I had issues was making sure the ads were serving. If the ad was not served, there was no "empty box." Instead, the next widget area moved up to fill the space. It also took a certain amount of time for the ads to actually start appearing on the page. This was due, not to the plugin, but with the Ad Manager. The ad manager had to recognize that there was traffic on the site, and equate that traffic with an Ad Slot before it would start serving the Ads.
Some Ads would show with in minutes, others would take several hours to start showing. I believe some of this was due to the number of page loads that took place.