The way that I do layers is by clicking "copy" on the menu on the left. Then, for the one on top, click there it says "normal" until it says "and". Then I color onto that. That might not be the right way to use layers, but it seems to work for me.
When saving pictures, click "auto save". If that isn't working, look and see what version of JAVA you're running. You might need an upgrade.