SOLVED!

I left the Scene layer ON. Now when I rendered a test frame, I was able to retain my AOVs *PLUS* have separate layers.

Original Post
I am trying to render an animation and composite it in After Effects. I want to apply glows to one layer at a time in post.

I thought that the Render Setup would be ideal but in a tutorial I am watching, it's advised to turn off the Master Scene. That layer contains Render Settings, AOVs and Lights. So is there an alternative way to render an image sequence with individual layers AND AOVs using the Render Setup? Or is tthere a better way altogether?