Hi Art, there are two solutions to your problem. First, make the layers before you make the scenes. In general, that is my work flow for every project. Draw the model, create layers, make layer assignments, create scenes. Of course that's for next time for you. For this project you could use a plugin called Add Hidden Layer. This will create layers that are, by default, hidden in all scenes. This works well for those scenes you've created already but for new scenes, you'll have to create the scene, turn the layer on and update the scene.
Irony: The opposite of Wrinkly