This is from Reuel Parker's "The New Cold-Molded Boatbuilding" from International Marine Publishing Company: "Epoxy is rolled onto both plywood surfaces and the deck is laid the same way as the first layer, including nailing off the perimeter. Take care not to trap air voids between the layers by walking around from one side to the other between the beams. Areas that separate or pull apart for some reason can either be screwed down in the field (removing and repairing the damage later) or be compressed with weights."

You could also borrow from stitch and glue technique by drilling two holes and tying the layers together with wire. Just be sure to push the pieces into position when you drill so the holes line up.