Hi,
The concept of Layers (at least in Capture) has got nothing to do with physical presence or visibility, it is merely a viewing filter used during the design process. If you wish to simulate the effect of objects changing their physical location or presence, then Scenes is what you want to be using.
One big difference between Layers and Scenes is that you can have each view in a different Layer Set, while the current Scene is a global setting. Also, each object can individually be set whether it is included in Scenes or not, offering a higher level of visibility and position granularity.