Since you are using a pantograph, you probably can not easily stop at the edge of the flange and restart on the edge of it, so I would recommend that you hand baste the flange down so it will lay nicely under your quilting.(removing the basting after quilting) However, if it were my quilt, and I took the time to piece a flange in it, I would not want it quilted down; I would want custom quilting to avoid quilting on the flange.