Answer:
First, come up with a storyline. This is the script for the animation. Then make the art. Then, you modify the art in a certain way depending on your animation software. Try looking in the "Help" Sections since I don't know which software you are using.
I suggest starting with http://Goanimate.com or http://Doink.com to start out. When you get more advanced, you can purchase this software:
http://www.adobe.com/products/flash.html
http://beta.toonboom.com/