First question, when was the last time the pads were replaced?
My wife's disk brakes squealed. I change the pads and they got much better. Then I sanded each side of the rotors to get them clean and roughen them up a bit.
Then, standing over top of the rotor/brake assmbly, center the rotor between the pads using the adjustment screws. There should be equal distance on both sides so when you pull the brake levers the pads contact the rotors at the same time and keep the rotor in a straign line. If they don't the rotor will flex one way or another. Err on the side of no rotor flex when adjusting even if it doesn't appear completely centered.