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Layers allow you to separate behaviors into multiple interchangeable Stacks. The idea is that the lower Layers are more stable and host Stacks that deal with static controller mappings (group, master faders for instance), choosing between or merging behaviors generated by the higher layers, etc.
The current layer is indicated via the Layer Indicator, shown below.
The Layer Indicator, found in the bottom right corner.
The result of the Base (lowest) layer is what eventually goes out into the Fixture. If you want to use generated Aspects from other layers, you have to employ the Source.Layer Block in your Stack.
Example of a Base layer. This one allows fading between the 2 layers above and full white while also giving you individual group faders and a master fader.