Once you have all the blocks sewn together sew your border pieces on. If you are short then piece them together before sewing the border on and then the tool instructions show how to start in the corner and it just falls into place.
http://www.junetailor.com/twistnstitchvideo.htm Here is a quick video that shows doing the border in a smaller version. Private message me if you still have questions. If I read it right, you were short on fabric for the border and that border has to go on before any cutting is done.