Synfig, like most every other competent graphics program, breaks down individual elements of a Canvas into Layers. However, it differs from other programs in two major ways:
1. An individual layer in Synfig usually represents a single "Primitive". ie. a single region, an outline of a region, an imported JPEG, etc... This allows you to have a great deal of flexibility and control. It is not uncommon for a composition to have hundreds of layers (organized into a hierarchy for artist sanity of course). 2. A layer can not only composite information on top of the image below it, but also distort and/or modify it in some other way. In this sense, Synfig Layers act much like filters do in Adobe Photoshop or The GIMP. For example, we have a Blur Layer, Radial Blur Layer, Spherical Distortion Layer, color-correct layer, bevel layer, etc...
Each layer has a set of parameter which determine how it behaves. When you click on a layer (either in the canvas window, or in the Layer Dialog), you will see its parameters in the Params Dialog.