This video teaches you how to render multiple layers at once using the movie render queue and proper organization. There is also a section on how to add post process materials to your scene to tie your renders better into 2D animated worlds.
A more in depth guide to rendering layers can be found here -
Cartoon PPM
Outlines PPM
Kuwahara PPM
Huge thanks to Edward Bennet for creating these open source post process materials.
https://dev.epicgames.com/community/learning/tutorials/dOGL/unreal-engine-beginner-tutorial-rendering-multiple-layers-2d-post-process