Organize Timeline

You can assign colors to groups of layers so they are easy to select. You can use the shy switch to show and hide layers that you have finished editing. You can also pre-compose, and that's not a bad thing. It allows you to not only organize, but can change rendering order, actually speed up render times, and greatly simplify organizing 3D layers and camera moves. You just have to get used to the workflow.

I assign colors to layers all the time. This lets me group layers that cannot be stacked on top of each other.  Learning how to use the flowchart is also a great way to navigate around very complex compositions. Many of my compositing projects have a half dozen nested comps (pre-comps) and hundreds of layers that would be impossible to work on efficiently without pre-comps or the flowchart.

Nevermind, found a workaround.