Meh, I just don't like using layers, they don't do much for me.
"What's that? Reason? Haha, what a bunch of baloney."
I'll just use this old drawing as an example (since it's one of the few drawings I've actually colored):
The left is with the colors on layers below the outline, and the right is the colors above the outline.
Basically it makes coloring a lot easier, you really don't have to try so hard to stay in the lines.
EDIT: I think it might be safe to assume you're using the paintcan on at least a few parts, which would explain the white dots.
