Most of the time, it's best to use HTML text as real text if possible. But occasionally, like with banners you'll need to add text to your image. This text, once it's saved as an image is not read as text by the search engines, but merely as just a graphic image.
Layers are a way to easily modify or change your graphic design. They make adding special effects to specific parts of the design very easy to achieve. Also you can delete a layer and not affect the rest of your design.