I don’t know how others do them but I always thought I would do one like a flip and sew row method. I would sew a row of the squares ( with the side pleats in) into a complete row. I would then sew the top (pleats pinned in) to the top of my background fabric. I would then top stitch between the squares to the background fabric. I would then stuff the pockets, pin the pleat in the bottom and to the background.
I would then sew the next row of squares together in the same way and lay it on top of the previously bottom pinned row, pinning in the pleats on that row also and then sew the seam between the rows to the background. I would then top stitch between the squares, stuff and proceed down the background fabric.