If you have a couple of layers of a scene (say, mountains in the back, a village in the middle, and some people in the foreground), just upload those individual layers into the Motion Book Tool.
Next, create a "parallax" layer.
Then, drop the background image onto the "+" button in the parallax layer's controls. Then drop the midground image onto the "+" button in the parallax layer's controls. Finally, drop the foreground image onto the "+" button in the parallax layer's controls.
The idea is that the parallax layer then has three "child" layers. When you click the checkbox "preview motion", you'll see the middle and front layers moving, and the front layer moves more than the middle layer.
The depth dropdown lets you play with how much motion there is in the back layers.
The absolute back layer doesn't move at all, so if you want your back layer to move a bit, just create an empty layer within the parallax layer, and move that empty layer to the bottom.
Here is a video tutorial demonstrating the parallax layer: http://youtu.be/K9Xp8fgq7Ac