I then add <div class="adplugg-tag" data-adplugg-zone="major_partners"></div> to where I want the major partner top banner to show.
The adverts are now showing, however the major partner banner ads (major partners) are showing with the side banner ads (side banners).
How can I remove the side banner ads from showing in the top banner section?
This can happen if you don't specify a Zone on your Ad Tag (or on your AdPlugg WordPress Widget). If your Tag or widget doesn't specify a particular Zone, the ad server won't constrain the results by Zone.
So I'm guessing that you hadn't set the Zone on your side banner widget.
I took a look at your site and don't see the major partner banner in the sidebar...and it does look like the Zone has now been set on your side banner widget, so I'm guessing that you've already solved it. If you are still seeing issues, please comment back or contact us here.