Start by ordering a set of cheap cardboard magazine files online. He will need a maximum of five. Line them up on a shelf in his room and label them: English & Maths, Sciences, Humanities, Languages and a final one for Extras.
Next, and armed with a glue stick, he needs to sort through the tatty paperwork with you, recycling what he doesn’t need, gluing what can be glued into his exercise books and filing the remainder into his magazine files with his school books. Those papers that are properly crushed but are still essential could be photocopied on your printer to breathe new life into them.
He should carry any random papers handed out in a slim cardboard folder in his school bag so that they remain flat. A handful of see-through plastic A4 envelopes should be on hand to give each sheet that extra level of protection.
As for the pencil case, check it every night for a week or so, getting him to sharpen pencils and account for anything lost that day. After a while his management of it will improve.