Trying to put Banner advertisements on Home page

[9Magazine]

Hello All.
I'm back again and trying to accomplish the task of adding more advertising to our home page. www.9magazine.com
I'm using a plug-in to handle the code and serving of the ad and have tried adding it to home.php...

The problem is that I can not seem to find the correct spot to add the code without messing up the whole page. I've been told that each section starts and ends with a <div> but that is not entirely true - is it? I've identified the spots which look appropriate - before or after the <div> but no luck. I can see the ad - but the whole right column disappears off to the bottom or makes a crazy allignment of the features.

Please help!