If the quilt is being machine quilted, then place beads or other embellishments on AFTER quilting. However, some parts of an "art quilt" may already have embellishments on them and so, hand quilting would be needed so that those beads, etc. could be carefully worked around.
Quilter's knot? That is used when hand quilting... yes, you need to 'bury the knot" firmly under the surface, so that the quilting doesn't become undone.
Good luck.