Ideally i think it would be best to cut both sheets at once for accuracy's sake. But as mention, its a bit more difficult to do this. I tried this at first, but decided against it when i got to the first non straight cut. My jigsaw couldn't handle cutting the curve through 2 sheets. Something to keep in mind if you cut the sheets individually is that as long as you are recessing the other panels 1/2" to 3/4" like you typically see, its gonna be hard to notice slight differences in the 2 sides. Its only when you have pieces that are flush can you notice differences. Does that make any sense? If not i'll try to clarify.
-Kevin