My nephew has severe ADHD and some other problems that interfere with concentrating and learning. He is seen by a child psychologist and has an IEP at school. His school evaluates him every year, and this along with regular meetings with his teachers have been a good source of suggestions to keep him focused and moving forward.
Does your son have an IEP and do his teachers have suggestions to help him? Has he seen a child psychologist? My nephew's helps him build skills that are useful in school such as effective listening and interactions with teachers and other students.
In terms of organization, one of my parents (my nephew's mom is out of the picture and my parents help raise him) sits down with him immediately after he comes home from school and talks about what occurred in each class that day. They then help him organize for that class (e.g., put papers in the proper folder, with one folder per class; figure out upcoming deadlines). This is before any studying gets done (they help him with that as well by reviewing his work or sitting next to him and helping if he is having big problems). It takes a tremendous amount of time, but without it I'm sure my nephew would have flunked some of his classes.