I love working with stripes and all the fun things you can do, it's lovely even if you are not loving it.
To do an "invisible" knot I would use something like embroidery floss. Starting from the top, I would take my stitch, tie it in a square knot and then simply slide the ends into the batting -- sort of stitch in the batting for an inch, come out either side pull a bit, cut, and then release the tension and the ends should fall back inside the batting and shouldn't come out too much... and if they do it will be years after you have given it away!.