About 3D Composite Nodes
If you start combining several composite nodes in your Node view, it is important to understand how they work if you want to get the desired result.
There is a specific order in which you should set your Composite nodes. Each time you process images through a 3D Flat Composite node, the images will be merged together. Images processed in later Composite nodes cannot be inserted between images of the previous composite since it is a flat image.
If you used Pass-Through type Composite nodes in your network, the images will not be processed together before the final Composite. It is important to keep your final Composite as a 3D Flat Composite in order to read the layer ordering correctly.
The most efficient networking system for obtaining the desired result is likely the Pass-Through composite mode throughout the whole network. This way, you can create individual compositions to keep your network clean and organized, but process everything together at the end.