There are times when my sewing room looks like a crazy woman has been working in it. However, I have to clean up and put everything back in place otherwise I can't bear to go into my sewing room. I can't stand starting a new project in the mess of the previous one.
Right now my sewing room is tidy and my DH wanted to know where everything went. I told him back where it came from. I try to be as organised as I can and I do have a place for everything and make a habit of putting things back where they live as I like to spent time sewing and not looking for things. I have spent countless hours over the years organising my sewing room. This is not to say that there are times when something in particular can't be found.
I try to aim threads and fabric scaps at the bin to minimise mess on the floor and sweep the threads dropped before I leave the room.
For example:I have my machine embroidery threads filed in numerical order and each container is marked with the thread numbers. I use the colour card to choose the thread and then can go to the exact location and when I put them away, they go back into the rightful container so they can be readily found again.
I am sure there is no perfect system just whatever works for you.