One thing we did for my son that helped: we labeled absolutely every drawer and shelf in his room, and we have a schedule with a weekly cleanup. I leave him alone for the rest of it.
With homework, our rule is that "Homework isn't done until it is put away" DS doesn't get his privileges until homework is done, so it happens.
Keep in mind, no matter what system you use, you will probably have to prompt him through it: it wasn't until just this year (at nearly 13) that DS was able to do things on his own without supervision. You have to work with him to show how to sort the mess into piles, and the piles into the correct bin.
For instance, I told DS that there are different ways to clean: I like to start in one corner, clean it completely, and move around the room until it's done, but the way he finally preferred was to mentally categorize the mess and clean up one genre of thing at a time (e.g., all the clothes, then all the papers, then all the books, then all the toys.) You have to work with him to figure out what system will work for HIM.