Things can get tricky when you start to layer 2D and 3D layers in the same timeline. As a designer, you need to understand how After Effects interprets things so you can build your compositions correctly.
- When working in 2D, the highest layer in the Timeline is in front of all the other layers. The lowest layer is behind them.
- 3D layers are stacked based on their Z‑position value (assuming the camera is pointing at their fronts). This means that the object closest to the Active camera is in front of the other layers. This is true even if the layer is at the bottom of Timeline stacking order.
- Track and Alpha mattes must always be immediately on top of the layer they are matting. This is true for both 2D and 3D layers.
- Layer blend modes still follow the stacking order in the Timeline.
- 2D layers mixed with 3D layers are ordered by their spot in the Timeline stack.
- If two or more 3D layers have overlapping z‑position values, After Effects uses their Timeline stacking order to determine top position.
If you want to keep a logo bug or other element always on top of your 3D layers it's easy. Just place the element on the topmost layer in After Effects and don't enable the 3D switch. You can also do the same for a background layer that you want behind all your 3D layers. Just put a standard 2D layer at the very bottom of the timeline.
From the new Adobe Press book – Motion Graphics with Adobe Creative Suite 5 Studio Techniques