I can imagine the trouble you are having trying to bury a knot using perl cotton. I don't think it is possible to "pop" it in with that heavy a thread. I think I would try bringing my unknotted thread tail into the batting then taking a backstitch as my first quilting stitch then quilting as normal. I would try leaving a fairly long thread tail buryed in the batting. For ending I would do the same, take a back stitch then take a stitch that is extra long that is buried in the batting. I would bring my needle up in the back and trim the tail very close to the backing then you can ease the tail back into the batting layer from the back.