On a Shearwater, does it matter what order I lay the three layers of glass on the hull?

Yes, it matters.  The first layer is the all-encompassing layer; the second is just on the bottom panels, and finally the bow and stern reinforcement.

There are two problems with doing that in reverse order: First, you might get an air bubble at the edge of the layers that end short. Second, if the smaller patches shift beneath the all-over sheet, you'll have the devil of a time getting them back in place.

You want to apply all the layers DRY, and wet them out with epoxy at the same time.