Begin by conferencing with his school counselor, all his teachers, you, and him to determine what exactly is going on and to work out a plan. Make sure that the school states what the consequences will be for not turning in the work -- failure, no sports, no extra-curricular activities, summer school, etc. Set up a weekly progress report to be brought home by him. Then you determine the consequences at home if he fails to bring home the progress report or he is failing to complete or turn in assignments.
Set up a consistent study time for every weeknight. There should be no exceptions, whether he has homework or not. There should be no TV, stereo, computer, or phone in his study area. Check his binder. Does he have a folder or section for every class? For awhile, check to see if homework is in the binder, the binder is in the backpack, and the backpack is where he will remember it everyday. Check his locker at school. Does it need some organization? Help him at first. Then, let go. Give him full responsibility. If he chooses not to take it, then impose the consequences.
You and he will become impatient, but overcoming two years of bad study habits takes time and patience.