Unfortunately Mackie Control does not support multiple layers of controls. It actually works as a different type of control system, which doesn't need multiple layers to accomplish the same number of tasks.
The Channel and Bank buttons will allow you to move up and down the mixer by either 1 or 8 channels at a time, and other options can be accessed by specially programmed function and transport buttons.
Layer 1 is specifically built-in to support Mackie Control, while layers 2-4 are designed to be mapped by the user with custom MIDI values. You can assign the value of all controls in layers 2-4 by using the included iMap software.
Only layer 1 works with Mackie Control protocol. If you find yourself unable to use the pre-mapped Mackie Control features, make sure you have selected the Layer 1 button to work in the correct mode.