I do knot and bury my threads when I machine quilt. It dies take extra time but it is what I prefer. Since I have to stop and reposition my quilt at the ends of rows, I usually knot my threads as I go.
I leave about 3 inch thread tails, pull both threads to one side, knot the tails together in a double knot, use my easy thread needle to go into the batt right where the sewing ends, run the needle about an inch through the sandwich before coming back up, pop the knot into the quilt and snip off the extra thread.