I was really worried about ds1 starting secondary, because he was just as you described.
Top tip #1 get a bag with plenty of pockets in so that everything has a home. Plan the bag packing for him, then talk him through it and get him to do it.
Top tip #2 Make sure he has a secure and consistent place to store his wallet and a specific place to put his rail ticket/pass in every time, immediately. Also house key if he needs one and a pendrive - both ideally attached to bag using a lanyard or keying.
Top tip #3 have two pencil cases. One small one with the basics - pen, pencil, small ruler - that is stored with his planner in the most accessible pocket in his bag. The second has "other stuff" - calculator, coloured pencils, scissors, glue. (My boys find having their own gluestick invaluable, cos they're not waiting in lessons to use class ones.)
Top tip #4 Label everything with his name and form.
Top tip #5 Have an emergency envelope with spare cash for if he loses his dinner money, wallet, trainfare home etc. Plus 20p coins to make a call if he needs to.
Top tip #6 Tell him you will replace the first item he loses, the second you will pay 50% and anything subsequent he is responsible for. With this rule my boys took much more responsibility for their stuff AND when they did mislay anything, were motivated to spend their break/lunch tracking it down.
Top tip #7 Get an opaque A4 plastic envelope. Tell him any letters home or loose sheets for homework go straight into it. That way they get home in one piece and he can get in a routine of checking it every night.
Top tip #7 Plan and expect to spend a LOT of time with him in the first couple of weeks. I was astonished at how much time I spent with ds1, discussing his day, helping him organise his school bag and the shelves in his room, getting him to tell me the tips and advice they were given in form and assemblies, making copies of timetable for his room, the hallway and spare copy for his bag.
Top tip #8 When you first see him at the end of each day initially, find out about his day. And ask about each lesson individually, ask if he got given homework and check if he has recorded this in his planner.
This may seem like overkill, but this investment of time and energy will pay off hugely in future. After the first few weeks, I rarely had to give either of my boys any support in getting organised: they just got on and managed it all themselves.
And my little space fairy? Well, he's 6'3" now, very self-reliant and independent, just about to start sixth form and got astonishingly high GCSE results in all subjects. Good luck!