In a medium bowl, combine 1 3/4 cups of the flour, the baking powder, baking soda and salt. In small bowl, blend cocoa and remaining 1 cup flour.
Begin layering: Spoon half the flour-cocoa mixture into jar. Press down to flatten (a small spice jar works well). Spoon half the plain flour mixture over cocoa layer; compact. Repeat. Top with brown sugar layer and granulated sugar layer, compacting each. Spoon M&M's over sugar.
Toss together both kinds of chips in a small bowl and add to jar. Attach a note with baking instructions: In large bowl, combine 1 cup (2 sticks) cooled, melted unsalted butter with 3 eggs, 1/3 cup milk and 2 tsp vanilla extract. Stir in contents of jar just until mixed. Drop dough by heaping tbsp onto baking sheets. Bake at 350° for 13 minutes or until firm. Cool on sheet on wire rack for 1 minute. Remove directly to rack to cool completely.