Keep in mind the displaying of a layer on top of the base layer is going to be based on some sort of action, either initiated by Storyline (for example, the timeline reaching the end, a variable changing its value, etc.) or initiated by the learner (clicking on a button, moving the mouse over a specific region on the screen, etc.). So, you want the layer to display WHEN something happens.
What is the WHEN in your first example? After a certain number of seconds? After the playback head has reached a certain point (defined by a cue point) on the timeline? When the video stops playing?