How I animate sprites:
First I block out the animation, I usually do a loose sketch, similar to pencil roughs in traditional animation, and then I’ll block out the silhouette in solid colors. This is the stage where I get things to move exactly how I want them to, without getting bogged down by details.
After that, I clean up the line art of the template, adding an outline and details such as a face and fingers. Even if the character’s wearing a skirt, kimono or other bulky clothes, it’s still important to have the sprite animated “naked” so that the clothes can animate correctly in response to the body moving under them.
Then clothes and color are added on top of the template.
If the art direction calls for it, then shading is added as the very last step.