Hi Kenneth,
Our solution is similar to what you've outlined. We output each photoshop layer as a png and then re-assemble them in Xpression to be animated seperately.
But each png we export is 1920x1080 (even the individual pieces of our lower thirds) This way we ensure the positioning is always correct and consistent with the original design.
Depending on how many layers you require, you may consider cropping down from 1920x1080, but as long as each element is in its correct place relative to the rest of your design, your quads should stack perfectly
#XPression