Filters are rendered top to bottom in the hierarchy and bottom to top in the layer stack. When dealing with solid objects, there isn't much to worry about with the render order. But when you add transparent objects, the order becomes important. Essentially, you want to be able to render the rear object first, then the transparent object in front of it second.
One example of this that I ran into recently was car headlights and windows. You couldn't see the headlight bulb behind the headlight glass. Nor could you see the inside of the car at all. Adding these glass objects to a new layer let the inside of the car render first, then the glass render second. Problem solved!
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