I was able to choose which layer was rendered when using 2.79 Now that things are called collections, and layers are... layers. I can't exclude collections from certain renders while at the same time allowing the excluded collection to render in other layers.
For example. I have a freestyle layer and a basic render layer. I want some collections to have the freestyle outline, while other collections will remain basic(without freestyle). I'm using Eevee and have not figured out how to do this in blender 2.8