Having a fixed background does create the illusion that other elements scroll on top of it, but in reality it doesn't. Let's say you have a div that's 400px tall with a fixed background image. That will cause only 400px of the image to be shown, but when you scroll it will begin to show the top or bottom portion of the image when scrolling up or down. It's essentially hiding the other areas of the image until you scroll them into view.
Setting the background image behind the iPhone in the Slate template to "fixed" should do exactly what you are wanting it to do. If it's not, I'm wondering if you might have at some point changed another setting that would cause the image to disappear. Can you provide your public link so we can be of better help?