In almost every single The 39 Clues book, there are puzzles hidden inside the book, such as on the page numbers, or on the covers. i.e, in The Viper's Nest (series 1, book 7), starting on page 39 there is Morse Code hidden on the page. And on the front cover, there is the string MDIALAE=RC, and on the back cover this is ARGLEDRGAE, which when stacked it says
MADRIGAL LEADER = GRACE.
Who designs these puzzles?
Little bit of random stuff:
You can solve these puzzles and type the answer in on the The 39 Clues site.