Something to remember is polymer clay is soft and will pretty much pick up anything it comes into contact with, so keep your work area as clean as possible.
Good lighting is important too. Especially when working with smaller crafts like beads. And have all your tools within arms reach.
Now, tape down your wax paper, making sure you get all the corners pulled snug so the paper doesn't crinkle in the middle. Move your hands around on the paper after taping just to make sure it's secure.