Hi Matt, 

i just want to confirm the step that you are at.  first, i am assuming you have glassed the interior of the deck?   and that it was taped to the hull?

if that's the case, then you simply use a sanding block with 60 to 80 grit sanspaper to 'trim it' to be flush with the hull (you want to try to not sand into the hull, but just to use it to 'trim' back any overhang) and round over the sheer line.   you then would use a succession of 80, 100, 120 grit sandpaper on a ros sander to to smooth your deck cedar strips.

while it's not a wood duck, this is a picture of a hybrid i completed last year where i have just started my first round of trimming the deck and sanding it after it was attached to the hull.  at this stage, you may also need to make up some wood flour/epoxy putty to fill in any gaps between the deck and hull where they did not mate-up perfectly and fare those in as well as part of the sanding process.

h