We all know that when working in 2D, we all know that the highest layer in the Timeline is in front of all the other layers, and the lowest layer is behind them, but when you make the layers 3D, their order in the Timeline stack becomes much less important.
3D layers are stacked by their Z-position value ( assuming the camera is pointing at their fronts). Therefore, So the layer closest to the Active camera is in front of all the other layers, even if that layer is way down low in the Timeline stacking order.
There are a few exceptions to this rule: Track Matte layers must still be on top of the layer they are masking.
Layer blend modes still respect the stacking order in the Timeline. However, only the Advanced 3D renderer will properly blend intersecting layers in the blended layer functions in 3D space.
2D layers also are also ordered by their place in the Timeline stack.
If several 3D layers share the exact same Z-position value, AE will use their Timeline stacking order to determine which one is on top.