Hi sakisbates,
Whoops...sorry for getting distracted. Here's the example I meant to post last Friday:
This is the original setup, similar to the example you posted...
And here it is with a reference created of each rig layer and sorted...
The originals and references are the same but with different visibility settings for certain layers as shown here...
Here's a short recap for working with reference layers...
When editing the animtions, be sure to edit only the originals, not the references. There's nothing wrong about editing a reference but when you do this you break the synchronization with the original.
This is why I have the reference layers clearly marked REFERENCE and highlighted in orange, to remind me not to touch these layers for animation. Another way to prevent unintended animation is to use Synthsin75's Lock Layers script.
If you accidentally animate a reference layer and break the sync, you can re-sync it by r-clicking the layer and selection Sync Channels To Original. If you want, you can copy and paste any keys you made to the reference to the original before you re-sync the reference.
Hope this helps, and good luck!
P.S., as shown here, you can disregard everything I wrote about appending reference layer names...unless you use Layer Shortcuts, in which case you should modify the script as instructed.