As a compositing software, the purpose of Autograph is to create what’s called a composite image that brings together multiple graphic sources stacked on top of each other. In order to combine these into a single image, you will use a Layer Stack. To explain this concept, we'll use the analogy of a plate stacked with the different food items that make up a hamburger. Here we've numbered the food items according to their height in the stack, starting from the top. In the world of image, each level is called a layer. Here is a hamburger consisting of six layers:

If we position ourselves above it and take a picture, we can get an image of this food composition. Its content depends on the position of the food items in relation to the camera, their order in the layer stack, as well as the frame boundaries. This is defined by the composition format.

In Autograph’s interface, the Timeline is located on the bottom left by default. The Layer Stack displays the layer order from a side view. The Viewer is situated on the top right and displays the result of the layer stack from above.

Each layer in this composition uses a different image as a source. These images are saved separately on the storage unit.

Even though images are rectangular, some pixels are tagged as transparent through the use of additional information stored for each pixel, referred to as the alpha channel. This transparency allows you to catch a glimpse of the lower layers in the stack that are partially covered by the upper layers.

The notion of layers already existed in the world of cartoons long before the digital era. Images were painted on transparent films and superimposed. When calculating the composite image, Autograph ignores these pixels, and just keeps the tomato pixels below. Keep in mind that an image is always rectangular, and just because we don’t see the pixels doesn’t mean they aren’t still part of the image.
Just as we can change the order of the food items, we can change the order of layers in the layer stack by clicking on one of them and dragging the mouse to a different position.
For more information about compositions, refer to this section which goes into more detail.