If one box is inside the other box, then 5, as 2 pears would be inside the inner box, and 3 pears would be in the outer box. 5 pears total would be in the outer box (including the ones from the inner box)
Since the recipe calls for 5 1/2 cups of flower and Molly only has 3 3/4 cups, subtract 3 3/4 from 5 1/2 to get the remaining cups of flour needed to make the recipe.