I can't tell from the manual, but all the pictures I've seen look like the two pieces of 1x2 are laid endwise to the trunk side pieces--that is with the narrow dimension between the side pieces and the wider dimension against them.  (I'm assuming the endpieces are 1x2, not at home where I can measure to see if they have been planed down.)

Anyway, I need to be 100% sure I am correct before gluing the centerboard trunk together.  (Forgive me if the answer is easily looked up in the plans.  I am at work and that thought just occurred to me.)