I have used this method and it works really well. You put all your squares in a pile (this works really well with scrappy) and then you just start sewing the 2 pieces together until you sewed enough for the length. Then you clip the thread off the machine and go back to the first pair. Open that pair up and sew the next piece to the right side. When you keep sewing like that all of the rows are sewn together and they are connected to the next row by the threads.
I usually cut the rows apart at that point and press them in opposite directions so the seams nest when sewing the rowns together.