I am lucky enough to have a dedicated design studio where I can have my mess, where no one will bother it, and it won't bother them. If you are serious about jewelry design, make sure you have your own dedicated space for creativity. If you don't have a lot of room, strive for quality, atmosphere, and lots of organization! You will be surprised what a nice spot you can create for yourself with a nice chair and great organizers.
I have found that using the stackable drawers (the size that fits 8 1/2 x11" paper) work well to organize my many works in progress. Simply line the bottom of each drawer with a bead mat (cut to size). Each unfinished project then goes in its own drawer. I also place a note or drawing in the drawer to serve as a reminder of my design idea.
I would love to hear how you have designed and organized your work space!