The goal is definitely to have nothing on deckYou usually break it down as much as possible and strap all the big pieces together. Sometimes, the trucker will let you strap some of it to the trailer, depending on the design of the trailer and the size/shape of the bundles you want to secure to it.
When my powerboat was trucked from Massachusetts to South Carolina (long before I owned it), they removed the flying bridge and apparently strapped it to the trailer underneath the bow.
If you wind up with anything strapped to the deck or in the cockpit, it needs to be really well secured. If it comes loose, it can wreak havoc.