Colored boxes can be created in a Simulink model by placing an empty subsystem underneath an area.
Here is the answer on the layering subsystems issue. It is somewhat tricky. We order subsystems in alphabetical (ASCII) order, first by capital and then by lower-case. So the top subsystem starts with 'A' and the lowest one starts with 'z', and so on.
Here's a good method for making the layers:
1) Start with the top layer:
2) Make a new subsystem.
3) Title it 'z'.
4) Set the background color with right click -> Background Color
5) Hide the name with right-click -> Format -> Hide Name
6) Open the subsystem, delete the ports.
7) Right-click -> Mask Subsystem
8) In the mask drawing commands write "disp('')" - this will hide the simulink symbol.
9) Repeat for the next layer, calling it 'zz' and so on...
You can see the attached model as an example.
