Mix the flour and baking soda in a bowl and set aside. With an electric mixer or stand mixer with a paddle attachment, cream the butter and sugars together. Add the egg, egg yolk, and vanilla and mix well. Gradually add the flour mixture and stir until a dough forms (may take a couple minutes of stirring). Fold in the pretzels, butterscotch chips, and chocolate chips. Do not overmix the dough at any point in this process.
Chill dough for at least 30 minutes (or up to 5 days) in the refrigerator. Drop by tablespoonfuls onto ungreased baking sheet. Press a few more pretzels (or butterscotch chips or chocolate chips) onto the tops for decoration. Bake for 8-10 minutes or until edges are slightly browned. The centers should appear very soft and puffy. Let cool completely and enjoy!