Amanda and Maria, I had the same need. What I did was to add a control button to the base slide containing the video, with the following triggers:
1) pause the timeline on the base layer when the button is clicked (on condition that its state is Normal, i.e. it hasn't been clicked before the video starts playing - I have a start button superimposed on top of the video that must be clicked in order to start the video, so that the user can start it when he/she is ready, and I don't want the user to start playing the video through the Pause button while the Start button is still superimposed on top of it),
2) resume the timeline when the button is clicked again (on condition that its state is Visited), and
3) to change the button's state back to Normal once it is clicked if its state is Visited (but that is just to be fancy, as the wording on the button changes from "Pause" in its Normal state to "Play" in its Visited state).
As it is, each time a cue point is reached the video pauses automatically while a message is displayed, but adding this button too also allows users to pause the video at any other time of their choice.