6th grade is a transition for all of the kids. The switching classes, a different teacher for each subject.. This is what middle school is all about. It sets a foundation for him to get through high school and college.
The teachers know this, but do expect the students to either figure out a system or the STUDENT to ask for help.
What you can do at home is to "guide him" in figuring out a system that works for him and then step back. He has to fail sometimes. Do not "save" him. Let his teachers know you are going to assist him, but you want him to figure out that there are consequences and HE is responsible.
He will not be failed for not turning in his homework on time. He will just get a lower grade. He may not make the first honor roll for the first time in his school career! This will not affect his standing in advanced or accelerated courses.. this is when he learns consequences. He will "own:" his grade because he has not figured out a system that works for him.
This is a safe time for this. His disappointment in himself will be hard enough. But you can continue to take away the extras as you are doing if you feel it is making a difference.
To tell you the truth, we did not ever punish our daughter for this. She was upset and disappointed in herself already.. She "HAD to be on that first honor roll!" It was her own goal. She would beat herself up over it so bad, we felt it was punishment in its self. If they turned in their homework late, it was still graded, but they lost 10 points per day! We knew she was doing the work, but had not figured out HER system yet. I told her teachers that I was not going to save her and they were all on board with this. They told me they knew she was bright, but just disorganized.
When he does turn it in, congratulate him and ask, "what is your system?" "Do you think this is going to continue to work for you?" "I am bet you are glad it is all getting there on time."
When our daughter was in 6th grade, she found that having a separate folder for each subject helped her keep up with notes, and homework assignments. Red for math Blue for Language arts etc.
On the inside the left side pocket was the "assigned home work" the right side was the "completed home work" ready to turn in..
Also the school gave every student an agenda. As you walked into class, you were encouraged to write down the assignments in the agenda. Any handout homework, went into her "subject folder".
If it was a "project" due in 2 weeks, at home she would plot out her goals.
Research, graphs, purchase supplies, completion.. Does not matter, she waited till the last moment most times!!! But I did not jump in a save her. She knew that I would assist her if she asked, but I was not the one that was going to run out in the middle of the night for supplies for a project she knew about for weeks before. She seemed to finally figure this out completely by 7th grade.
Your son will be upset with himself. He will be upset because you are upset. We always told our daughter, "we love you. We are not mad at you, but we know you can do this." Maybe start taking a step back on trying to save him. He is not a baby, but he is sensitive at this age. The hormones are raging. He is intelligent, he just is not totally mature. Give him space. You do not need to comfort him when he cries out of frustration with himself. He needs to learn to take these feelings and figure out how to handle this..
I know where you are coming from. Our daughter has always been an excellent student with very high goals, but I knew I had to let her earn her real grades now, because this was her education.
Hang in there.. This is so totally normal. It is a small bump in the road. Do not spend so much time focused on him. Give him some space. It is a change for you too.