For transporting boat the best, common and recommended option is a boat mover. What they do is they use a trailer or cradle to tow your boat into the ship and at the lower deck it is parked. This method of shipping the boat protect it from any damage while the ship sailing in the sea. Once the ship gets to the destination port, the boat can be easily towed off it and moved to the final destination.
This operation is called roll on/roll off process. In this process a specialized trailer is used to move the cargo as one piece from port to port. Sometimes a flatbed trailer is used to move it from the origination to the destination. Very less handling is involved in all this because there is no need to lift the cargo on and off the vessel.
Rather it is driven on, parked and then driven off. Being secured in vessel's garage decks during the voyage, there is no risk of damage due to water. Conclusively, Ro/Ro process can be said to be the most secured technique to carry out the transfer of an over sized boat.
Enclosed Boat Container:
Now-a-days a container in which a boat can fit is used transport it from places to places. Most of the liner vessels today are full container vessels. Your boat transporter will prefer to ship you boat in a container if it fits into a standard 40' long, 7'8" wide and 7'10" high one.
In case of a big sized boat, disassembly of some parts like upper cockpit, engine and bimini tops etcetera is recommended. Vessels which get fitted perfectly into 20 or 40 inch container are best for the cargo.
A flat rack and strap are used to keep your boat safely into the vessel in case of an over sized boat. The boat can be protected form damage or debris by shrink wrapping it.
Water to ship moves:
Your boat is loaded or unloaded directly from the water by your transporter.
Barge to ship moves:
Your boat is directly loaded and unloaded from the barge in the water to the ship by the movers.