Dave,
I have a lot of experience in packing both bulk bottles and in carton form. For bulk packaging, shipping on a container, we wrap the bulk bottles in plastic and place strong cardboard dividers in between each row and secure the corners with 5 layer corrugated cardboard. For cartons, we place the bottles in your custom design carton with partitions and then place in a master box to keep them dry while in the container. After they are on pallets we wrap again with plastic and secure the corners with 5 layer cardboard.
Please let me know if there are any questions I can answer.
Cheers!