Hi Hamlet G, hi folks.
In SketchUp (SU), layers are used only to control the visibility of objects.
Normally, you keep base geometry on Layer 0 and assign groups or components to other layers.
This is what you seem to be doing so, everything looks fine so far.
The easiest way that comes to my mind to manage various combinations of layers visibility or invisibility is to use scenes.
For example, suppose that you have a component called A. This components has two sub-components called A1 and A2. Now suppose that you want to show two options, one with only subcomponent A1 showing and the other with only subcomponent A2 showing. You create 2 layers that you can call whatever you want. Lets call then A1 and A2. You assign sub-component A1 to layer A1 and, of course, sub-component A2 to layer A2. Then you create 2 scenes that you can call whatever you want. Lets call one Option 1 and the other Option 2. On layer Option 1, you show layer A1 and you hide Layer A2. On the other scene, you show layer A2 and you hide Layer A1. Don't forget to update the scenes after changing the visibility of the layers. Maybe you can uncheck the box that tells the layer manager to remember the camera position. That way, if you orbit, pan or zoom between views, you wont loose that view when you switch option.
Once this is done, a click on the relevant scene tab will make visible the required layer and hide the non required one and thus, will only show one of the two sub-component, even if they are occupying the same location in space.
Just ideas.