Images that contain layers are saved in a special file format called SPH. Images saved in other file formats (such as JPG, GIF, etc) lose their layer information, becoming flattened. FotoFinish automatically saves layered images as SPH by default. In fact, before adding a layer to an existing image, FotoFinish warns you that you must save as an SPH file in order to retain the layers.
When you ultimately decide to publish a layered image (on the web, for example) you will need to save it in a different file format (such as JPG or GIF). But you should always keep your original SPH file around in case you need to edit the layers in the image.