I have finished my quilts both ways.
I don't care for ones tied on top of the quilt with knots, (only because my boys would make it a mission to lie in bed at night and untie them!)
I prefer to"tie" using a crows foot stitch just like my mother and grandmother taught me. The thread passes between the stitches in between the layers of fabric. It is great, no threads distracting from the pattern of the quilt and a great puffy look of a tied quilt!