Generally speaking, working with texture layers involves adding texture layers to a shader, adding ports to the layers, and then editing the layers' properties to control the textures they display and the way in which they're blended with other layers. For each layer that you add to a shader, you'll need to follow some variation of the following procedure:
Select a shader to which to add layers.
Add a texture layer to the shader.
Add shader ports to the layer. You must add a port to a layer in order for the layer to affect the port.
Edit the layer's properties to define its color and mask inputs, and adjust how it's mixed with previous layers.
Repeat steps 2 to 4 for each additional texture layer.
You can work with texture layers using the texture layer editor, using the material panel, or using the render tree.