Looking through La France Maritime au Temps de Louis XV et Louis XVI: Gravures et dessins des frères Ozanne. Peintures de Joseph Vernet by Alain Boulaire (ISBN 2-911468-75-9), there are many images with barrels. It seems fair to say that there is no one way to transport barrels — they were loaded as people thought convenient, and not always with the head or bilge down.
The first image (p. 60), show a barrel on its head in the stern of a boat.
The second image (p. 68) shows a barrel resting on its bilge on the thwarts. I always prefer to get the center of gravity lower, and I can’t decide if the barrel is in the process of loading or unloading, or they would rather have the easier time of moving it from the thwarts than of lowering it and raising it.