How to get Panels to override node with "no extras"
The problem is (I think) that when you added content (Whichever Variant -> Content -> Gear -> add content) you clicked Node and then Node content.  Node Content will display all of the content of the node (Title, Body, and all Fields).  If you just want to display the body choose Node body.

Then in another Pane (Panel Biggest -> Region -> Pane Smallest) you can add your other fields.

Here's a video that talks about Panels and Panels Everywhere and can help show this in action.

http://www.youtube.com/watch?v=v6zMcfTxkhc

Hope this helps!