Layer work is mostly done (it may needs some testing and fixes of problems found). Right now have another view that you can setup your layers and for every shape you have the option to pick the layer by name. In the LayerView you will be able to manage layers, to override the scene colors if you want to pick by layer profile.
Some nice tricks are in this dialog like: every time you pick Add Layer, a random color is generated, another part is that Remove button will be disabled for current layer, and so on.
So you may try this functionality via nightly build.
P.S. The color theme is on my machine, so don't feel attacked for it :)