Magazine Style Header Ads Different Pages

I have the ad rotate plugin installed so I can track the clicks on my ads in the header and have a new one displayed as the page refreshes.  I had to insert the ad rotate code within the themes header-top-area.php file to get it to display.  Now my issue is, I'm stuck with the ads only in that category.  

I've created a custom layout template for use on several other pages for a course I'm building and only want to show certain ads on those pages.  Is there a way to target just that custom layout header ad space? 


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