Personally, I think you should keep all the bones in the same layer. It may seem more organized at the moment but in practice, it forces you to switch layers more often during animation.
I tend to set up fairly complex rigs at work but I always try to minimize how much jumping around I'll need to do for animation. For example, many of my switch layers are SBD driven so I can animate them along with the rest of the bones in the rig on the same layer channels.
That said, now that we can edit multiple layers and use Tags to call up layer sets, maybe that's not as big an issue anymore.
