I get the impression you have already glued the boards together. It wouldn't be worth the trouble to cut them apart. The two boards you have may not warp even if you didn't alternate the grain. It's just safer if you do alternate the grain. While it's true if you alternate the grain the panel is less likely to warp when I glue panels I'm more concerned with matching the grain so it looks like a single piece of wood. Normally it's when you make a large panel like a table top you need to be more careful.