The built in adsense integration was made to be very simple for admins with little experience to use as an easy way to ad ads to their forum- and it does that job fairly well.
When you need more advanced options like in your case you should simply be using the ad-location templates and the code direct from google. Combined with some simple template conditionals you can specify exactly what forums and threads to show ads in or not. It's only marginally more difficult then the built-in integration to begin with.
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