The Digital Photography School blog has an instructive tutorial on using layers for those just getting their feet wet inside Photoshop, or other high-end image editors like the open-source GIMP ...

It'll let you organize and arrange your layers, set blending modes, set visibility and opacity of layers, group and merge layers, and a bunch of other neat things we'll learn about in future lessons.

This tutorial demonstrates a versatile and flexible technique that will match animations between layers you choose to connect to enhance, simplify, and accelerate your animation process.