My top layer is showing above my bottom layer

In general layers that are above (have the lower layer number) are rendered as in front of the layers below them. That is how pretty much all layers work in Adobe applications. 

While the correct answer works it is at best a work around. You shouldn't have to add a new layer to get 3D Layer stacking to work for you.

Mylenium is correct when dealing with only 3D layers the layer stacking order (order of layers in the timeline) is mostly irrelavent and it is the z-position (3rd number when you look at position) that matters.

So a layer with a z-position of -100 will always be in front of a layer with a z-position of 0. 

The ony time the layer order matters are if two layers have the same z-position. Say two layers both have a z-position of 200 whichever layer is on top will be in front.

3D layers are shown based on their actual depth stacking, not the layer order in the timeline. You may need to adjust the Z value. Anything else will require a proper screenshot and possibly other info. No point talking about invisible elephants.

Mylenium