The easiest way I can describe it is to go ahead and take the stitching out. Lay the top and the batting but not the back. You only need batting on the area where the tracks are, so scrap batting works great for this. Also poly batting works better than cotton because it has more loft. Stitch around the tracks again. I use water soluble thread at this stage. Turn it upside down and cut the excess batting outside of the tracks. Make your sandwich again and quilt as you were planning. I would suggest to use a much heavier quilting outside of the trapunto area to make it pop up more. When finished spray the quilt or go ahead and wash it to make the water soluble thread dissapear. You could leave it and it will go away the first time the quilt is washed, but you may have double lines for a while. If you decide to wash it, while it is wet you can block it, square and bind. Please feel free to ask if this was not clear enough.