It's important to set up your working area cleanly and as organized as possible. Have plenty of working space for your supplies, and arrange your tools within easy reach. If your workspace is not brightly lit, or if you are working at night, have a work lamp lighting your area.
Use a removable working surface, such as this double sided microfleece pad. This allows you to clip wire cuttings onto one surface, then easily whisk them away when you are done working and over to the trash can.
Keep at least one sorting dish. This will help you to have an ease in selecting beads, and helps keep your work area neater. I use a stainless steel ramekin.
When storing beads, choose containers that open and close individually within the sections. Often, you can also find a locking mechanism on these containers, and I highly recommend taking advantage of this feature. Keep like beads in the individual sections of the attached containers in order to make finding a specific element easy. I keep all my silver plated findings in one, all my gold plated findings in another,and my faceted glass, my seed beads, and all my gemstones in others. When laying these containers out, I keep them in piles of metal findings, glass, and gemstones.
Keep a few tiny baggies for storing projects in process or bead overflow. Store everything in one area, and put it back as soon as you're done working. This is a safety feature, as well as a way to not make a mess or lose beads!