A layer can be defined as a transparent surface upon which you can draw one or more shapes. These shapes are thus associated with their corresponding layer. All canvases in OmniGraffle have at least one layer.
Think of a layer as a transparent plastic sheet where you draw with a pen. If you now visualize that you can put another transparent plastic sheet over the first one—and draw on this second sheet—then you'll have the concept of how canvas layers behave.
Let's say you have a diagram of your new company office. The bottom layer will then have the outer walls. You could the have a layer on the top of this outlining each office cubicle, a layer with the electrical wiring, a layer with air conditioning ducts, and so on. Then you could have yet another layer with the office furniture in place.
So if you wanted to show only the electrical wiring—you hide the layers with the office cubicles, the office furniture, the air conditioning ducts, and so on. Then, if you need to show...