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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

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You can assign Freestyle line sets to collections, this would allow you to apply the effect selectively.

Freestyle settings

For the other part of your question I believe this post should answer your question for the transition between 2.79 and 2.8. The general idea behind the scene and view layer concept is explained in this post on the Blender Developers Blog.

Let's say you have a scene with a collection called "Only once" that you would like to include in one view layer, but exclude in another. The view layer where "Only once" is visible is called "View Layer" and the one where it isn't is called "View Layer.001". You can have the collection "Only once" it both view layers and have it activated in one and deactivated in the other.

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In order to exclude specific view layers from rendering in the scene, you'll have to switch to the scenes in the outliner.

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If you activate the restriction toggle for rendering you can then exclude specific view layers by clicking on the camera icon behind the collections name.

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