When joining Warm and Natural, or any other batting needle-punched through a scrim, try to make sure the scrim side is facing the same direction (up or down) on both halves. It will affect your ease of quilting.
When joining non-needled-punched batting, make sure the grain is running the same way on both halves. The batting grainline determines which direction you quilt first and should run parallel to the grainline of your fabrics for stability.