Some people are a lost cause, I'm half that way. My kitchen and bathrooms are generally very organized, my living room is now that my baby is crawling, but the bedrooms are disaster zones, FEMA would probably be interested in them!
Kids have to be taught how to be organized and it's something you have to work with constantly. It's something you have to have a system for. Places for everything, containers, organization has to be taught literally one thing at a time, from pencils to crayons in a box to backpacks. I take away my son's backpack periodically when I see that he's just shoving papers in it and he has to carry his papers in his hands.
I didn't grow up around organization, so I'm most comfortable in controlled chaos. You should try to set an example in some areas, start small. Have your son help with dishes, a simple chore where everything has a specific place. Every day have him do something to get organized. Get shelves, boxes, tubs, hooks, etc. and teach him step by step where things go. I'm just now starting to get myself organized, and I've got 5 kids to keep up after! Be an example and work WITH your child as you help clean and organize. And be prepared for a long haul, it takes much longer to unlearn a bad habit than to learn a good one from scratch!
Also, give him some space to be totally disorganized. A drawer in a dresser, a toybox, a plastic storage container, somewhere that he can just "dump" stuff of no importance. I know that helps me to have dump areas that I can just put stuff I don't know what to do with.