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I believe that with the new salt and pepper shakers, the salt shaker is the one with 3 holes, while the pepper goes in the one with 2 holes. Salt is used more than pepper anyway. Pepper should only ever be fresh ground at the table, meaning salt shakers win out.
Fill the right shaker with the right seasoning. Some say that salt needs the container with less holes but larger ones, because it's the bigger grain to get through the holes. Others prefer the salt to have more holes but smaller because it allows for more of the seasoning to flavor the dish.