Basically just use the 'raised side' as the right side and the smooth side as the wrong side, putting it together just like doing regular quilting cotton fabric. To get the corners to lay exactly where you seam/join it will take some doing with measurements, plus -- because it will be a mitered corner since you are doing it all in one long strip, it will be really bulky at the corners to have the joins meet there as well.
I would just join into a long strip and let the joins/seams lay where they fall. With a binding (narrow) it's not something that will stick out once it is all together.