I completely agree with spanglystarfish too - great post - and I have noticed some comments on other threads that are quite hurtful. Saying someone "should" be able to do something is not helpful and one of our jobs as parents is to help and support our children acquire the skills they need - whatever their baselines. With organisation, if you get behind at first it can be very difficult and stressful trying to catch up.
Minidipper, I feel your pain. One thing I think is really important is to decide WHERE they are keeping all their books: at home or at school. Having some in each place is the worst of all worlds. You could get a big box in the kitchen, put everything in it, then help him pack each night. Or he keeps everything in his locker (if he has one), and then at the end of the day he must go there and drop off everything he does not need for homework. Then in the morning, he drops off last night's homework books and collects the books he needs for that day.
If you can't decode the timetable, I would email the school today, explain the problem and ask for one in plain English with homeworks on it too. This is a really vital tool and also a security blanket - by half term he probably won't need it but it will help him now, and using it will help him practise the organisational skills he needs to develop and gain independence (so he could talk you through the following day, when he will go to his locker, what he has to remember at break). My dc get one full of gobblidigook and then their tutor decodes it and they write that one down in their planners.
It sounds like homework is taking too long. Are you around when he is doing it? If so, just for now, I would ask him what each piece is and check he is not going over the top (eg spending ages producing a lovely poster on the computer with loads of fiddling around). Just talking through what to do in what order, and what if anything to save for the weekend can really help. And I agree, it should be fine to put a note on saying he was exhausted and has spent 30 mins trying hard at this. I'd be really wary of hw spilling very into lots of the weekend - if this is an issue, I'd help him decide what time he will do it and then maybe try to do some childish stuff - whatever he's into - as I think going back a year or two can help give them that bit of extra security they need.
Sorry this is such a long post. You are doing all the right things and it does get so much better, and you will be so proud and happy when you see him in year 9 sorting everything out, making plans, seeing them through. Do not feel bad if he needs a little help now to set him on the right path. I also have known children who appeared to manage fine alone, but when the going got tough in yr 11 or whatever, it turned out they had not really been organised - just clever and fast readers - which isn' t quite enough to organise your own revision etc.