Hi JL,

  I have only built from plans but seeing that no one has responded yet I'll add my .02 and bump you back up. I would think you'd treat the epoxy here the same as a scarf, that is treat the bare wood first with unthickened epoxy and before the epoxy sets apply a lightly thickened mixture - much thinner than a fillet more like a molasses consistancy. Use enough to fill the joint and keep in mind excess will be a pain later. You may experiment with different filler mediums to find a closer color match, the wood flour alone may be darker than your epoxied ply.

  You used the word 'glue' but meant epoxy, right?

  Hopefully someone with experience in puzzle joints will chime in here soon.

You should use epoxy thickened with silica. The kit instructions do give the details - scarf joints are right for plans builders. For the kits I've done, they also required fibreglass tape on the inside face. For a neat job, mask off either side of the join. Then do the jigsaw edges generously with silica. Put the tape strip over, and wet out with unthickened epoxy.

Make sure the building table surface is flat under the joint, and weight the boards so they stay FLAT. You can also hold them down with battens laid over, and screwed to the board. 

Don't be tempted to move them till the epoxy is properly hard. And make sure you do a left and a right!

Scratched my head over this one a little bit---Pages 42-46 in the Skerry manual detail the assembly of the puzzle joints.  Just thicken epoxy with a little silica, daub it on the joints, and press them together.  Voila.

A little sleathing reveals that you probably got your Skerry kit in the UK, so it might be that the UK-issue instruction manual differs from the Yank version.