Tracking with Channels
There are no hard-and-fast rules for ad layout and ad placement—even the AdSense heat map is just a suggestion. Publishers with similar layouts report vastly different clickthrough rates. Ultimately, you have to figure out what works best for your site.
The easiest way to figure this out is to use AdSense's channels feature. Channels let you track ad or link unit performance on a per-page basis and/or on a per-unit basis. You can define a custom channel for each ad format and an URL channel for each page, for example, and track very detailed information about the ads you're displaying on your site. Armed with this information you can fine-tune the ad layout and placement for better long-term results.