Layers in Paint.NET work a lot like a stack of paper, as you'd expect.
As you've said though, you want to know how to. So to begin with, make sure your layer window is open. You'll see a little square with a + on the bottom bar of that window. Click it and hooray, you've got a new layer. Now you can click between them using the window, and whatever changes you make on that layer will only affect that layer. Suppose you want to overlay a picture of a plate onto a table. Create a new canvas, make a new layer. Go to your first layer (the bottom one) and then paste in your image of the tabletop. Go to the top layer and paste in your plate image. You can move this plate around however much you want and it won't affect the table. If it has a background on it, you could use the magic wand tool to remove it. Note that in the layers window there is an image of a nametag and pencil where you can change the opacity and blend mode of the layer to the layer/s below.
Hope this crash course helped!