Flash layers are arranged from the bottom up, and so that's how visibility is determined, as well. The first layer on the bottom is your base layer; anything you layer on top of that will obscure the layers underneath it.
You can create a new layer by clicking the Insert Layer button, at the bottom to the farthest left; the new layer will appear above the currently selected layer. In order to change the layer order, just click and drag on the layer. To delete any layer, click the little trash can icon for Delete Layer to the lower right corner.
The Add Motion Guide button lets you do just that: add a motion guide to control the motion of the layer below/linked to the guide.
