Next time you glue up a box, clamp it down to a flat surface so it doesn't get twisted. If you have the top flat, place that on a flat surface. Then cut a block of wood or use dividers that you use to scribe around the box. This will mark the bottom parallel with the top. Depending on how much it's out, you can cut or plane to that scribed mark. I'd use a low angle block plane for minor adjustments.