I guess if your problem is that the whole boat is not as secure now that it is flipped over, the obvious solution would be to make it secure. Make a good set of cradles and maybe hot-melt glue the hull into the cradles so the whole thing won't move and continue in the same way you did the hull.

However, if you are looking to make large panel for the deck and then using those panels to make the deck in the manner of a stitch and glue deck, I think it should be possible and the results could be very good as long as the shape of the deck permits it.