Are you trying to add the ads to your pages without changing the html of the pages? You only need to use mod_layout if you want to do this.
You can do what I think you're after with PhpAdsNew relativelty easily if I understand what you want to do properly, or even using RMX-Direct (
https://direct.rightmedia.com/ ).
I'll have another read of this a little later and try to explain what you need step by step, but I'm in the middle of moving house right now
-Tim