I use the styrofoam trays that meat come on, the big ones hold exactly 20 stacks, then I cover with plastic cling wrap and put in bookcase where the cats can't get, well they haven't found them yet!
My male indoor cat Stewie, loves knocking over the beads when I am making necklaces, and I think he hides waiting for me to get up and leave them alone for 1/2 a second. All over the floor in no time, I don't work with beads much anymore. Bella is the one who will make a mess of the thread, or rolls of ribbon. I finally figured out that she thinks she is helping, so she has her own roll of ribbon, and she is so smart she knows where I keep it!
Both of them will find ways into the sewing room no matter what we do, so I have given up and just let them roam freely, they are good company at night when I sew and they are so funny! if they get to close to the sewing I get out their laser light, they will chase it for hours.