Please feel free to ask any questions about the template here... I shall be giving out hints, suggestions or providing simple explanations. Just ask, and I will try to get back to your queries as soon as I can.
#1 - Do remember to check out the sprite objects since quite a number of instance variables are in play.
#2 - The top most layer stays fixed in place because the Parallax setting is 0, 0. Hence, it's name - User Interface (or UI for short).
#3 - For now, please note that the Missile Trail object (a 2x2 sprite) is overlapping on top of the Alien Missile sprite; to select it, use the Project Bar. We shall issue a new version later to correct this.