when i bed the pads in,
i use the brakes really hard,
find a quiet well sealed road, get the bike up2 at least 60k's
and brake really hard they wont lock up but still be careful,
do this 3 - 4 times the higher the speed the better 80-100k's.
i do this for car brakes as well.
you can try this method if your pads squeal, sometimes it works.