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Oh gosh, I'm just as horrible at organization.

I find making a timeline helps a lot. Plotting out when events happen really helps when organizing chapters (especially when the chapters are focused on different people). I use Anne McCaffrey's Dragon Riders of Pern series as an example for how to organize chapters.

I also write up a short summary of what I think I want for each chapter. That way I can remember what it is I'm trying to accomplish.

My desk is covered in scratch paper cause I can't seem to be able to keep my notes organized.

Okay, looking at your work space, my first suggestion would be to get everything off your desk that is not story related. All of those stuffed animals, nicknacks, books/papers and such that are not related to your current project. If need be, just put them all in a box and set them on the floor, or better yet, in your bedroom. I'm guessing you only use your bedroom to sleep and get dressed in, so that shouldn't be too much of a problem.

Your desk should have items related to your story. Whether those be pictures, books, items, or whatever. Don't clutter your space with things that will distract you from your story ideas.

I love the chalk board idea a lot, and I can understand you not wanting people to see your story ideas. My only suggestion for that would be to get a light piece of material from a store like JoAnns, and tack it up to the wall in a manner that you can let it drape down over the boards when you don't want them seen, and held up when you are working, and need to see them.