Click the button on each render layer to set it as renderable. Upon batch rendering, a separate folder is created for each render layer that is set as renderable. In addition, a masterLayer folder is also created. Render layers not set as renderable are not rendered.
For example, if two of your render layers are set as renderable, and one is called character, and the other called room, then after batch rendering, three folders are created in your image output directory as follows:
Batch render scene files with either render setup or legacy render layers without having to switch the Preferred Render Setup System in your Maya preferences. For more information about the two systems, see Render setup versus legacy render layers.