It's preferable to have the boat bearing against the wide part of the board, so the weight is spread out over a larger surface. In extreme cases, like, years of use, or having a lot of weight in the boat when you put it on the trailer, particularly if it's a thin hull, the skinny side would be prone to deforming the hull. Again, most of the factory-built trailers I have seen using 2x4's have the board with the flat side bearing against the hull.