Organization takes time, but eventually, it saves time because you aren't constantly trying to locate a particular tool or material you need. The first tip for getting organized is to pick one spot in your home that will be the primary work space for your jewelry designing. I realize this is difficult because space is limited in most homes, but if there is any way you can even find a corner of a room that you can claim, do it. I can't help but think of Virginia Woolf's famous work A Room of One's Own when I think about this issue. Basically, she claims that one of the most important elements to being a successful artist is having a place to be creative. If you are serious about jewelry making, even seriously as a hobby versus a business, then you need to allow yourself a space to create.
I'm very lucky that I have a bedroom to use for this. It's a combination office and studio space now because I have my computer and other equipment in there. Next to my computer area, I have a workbench that used to be a computer desk as well. The keyboard drawer is perfect for storing beading trays when I'm not working, keeping them protected from my office assistants' little paws. There's also another drawer for tools like scissors and hammers.
