Large Motion Graphic Project: Workflow issues, do my layers have to be 3D layers?

The project that I am working on is going to be approx. 3 minutes long, and it has a load of elements that I use. If I had to guess I'm using about 50 or more. This makes the workflow a little tedious. I somewhat manage this by using the shy mechanic and colour labels.

One of the problems I'm running into is when I precompose multiple 3D layers, I loose the composition and things disappear in z space. I will admit that this is my first large project and I am still testing out the waters. I continue to do more research to maximize my workflow, but one of the ideas I have had, is since my project is very linear, and none of the elements do any tricks in z-space, am I able to make all my element layers 2D to keep things organized and in the proper order? So then I would just keep my Camera and Null as 3D Layers to continue the camera movement? Would this work?

I am also looking at some plugins that will help me manage all my elements, like SureTarget by VIDEOCOPLIOT

Thanks for your time.