If I want to limit an effect to a certain shape or portion of the page, I would usually use a mask. In the design for Fluther, I would use a mask to fade the opacity of the dark background pattern as it moves towards the bottom. The same is probably used for Mr. J’s ‘shiny’ effect up top in the header. Used another way, if I wanted to add a hand drawn highlight to the ‘Question’ bar, I would mask that in my mockup so it would appear only in that portion and not on the layers behind. Does that help?