I'm soffy, maybe I mis stated the issue... The ads are showing in the correct zones & places, but they are also showing an additional set (which we don't want) below the footer.
I have Zones setup for Ad Plugg Network, however the network ads are showing under the footer of all pages on my wordpress site.
The "z-index" controls how different layers on a web page are stacked. Your footer must have a really high z-index. Try adding the below CSS rule to your stylesheet to get the AdPlugg ads even higher.
.adplugg-modal { z-index: 99999; }
If you use WordPress, you can modify your stylesheet from your wp-admin by going to Appearance, then Customize, then Additional CSS.