Simple answer: Pre-compose. You need to try and understand how AE's rendering pipeline actually works and how it is affected by layer switches and all that stuff. Trying to do everything in a single comp seldom gives the result you want.
Hi Mylenium and thank you for your help. I tried pre-composing but it's not helping. Within the pre-comp none of my layers have 3D activated. After precomposing, I turn on 3d and add a camera. But as soon as 3D is activated on the precomposed layer, I suffer a resolution hit. It seems to be an either or situation - either keep the high resolution and stay in 2D or go 3D and see my map pixelated and my stencil alpha reversed. I'm looking for tutorials but haven't found any yet regarding my issue. Thanks again for your help.
You know you do not have transparency enabled, right? So that blue background that you think you have is for preview purposes only and is going to render black. Of course once you enable transparency and set up a proper background you may discover that Stencil Alpha is not the way you want to go.