Okay since none of you understand, Here's how it works.
Layers in Paint.NET work as if you have one picture below a transparent glass, You can't try to erase the below picture, But you can draw on it.
You cannot use them to make GIFs automatically. The way making gifs work is by making seperate images, Drawing on them, Then saving each one. Then take an GIF maker and fuse the frames together. And that's the only way to make GIFs in Paint.NET, Unless you have a plugin.