Jopedder,When I railroaded in New Zealand during the 70's, one thing I did when based for a couple of years in Wellington was switch the rail ferries that plied Cooke Strait between the North and South Islands. These vessels carried rail rollingstock, comercial and private vehicles as well as people (mostly tourists).
The ships reversed into their berths at Wellington and Picton under the control of the 1st Mate who conned the movement from a control station located at the vessel's stern. Once berthed, the stern door for rail traffic was opened and a LINK-SPAN (hinged at its shore-end) lowered to mate with the ship at rail deck level. This bridge-like assembly accommodated vertical movement of the ship relative to the shore and also permitted significant rolling movement of the ship.
The link-span had triple-gountlet track down its length, with the switch points back on shore prior to entering it. The left-hand set of tracks joined up with the port-side track on the ship. The centre tracks with the centre road on the ship, and of course, the right-hand tracks accessed the starboard side of the ship.
We would run the switch engine down the link-span and pull the centre road. This rake would be pulled back into the ferry yard and another pushed down onto the ship to replace it for the next sailing. Then the port-side would be pulled and as the rake was drawn off, the vessel would assume a pronounced list to starboard. This was overcome by the 1st Mate operating controls to pump seawater ballast from one side of the ship to the other. Of course the ship would right herself when the port-side track had a new rake pushed aboard and the ballast would have to be pumped again. The whole process recurred when the starboard-side road was 'pulled and pushed'.
Complete passenger train consists (separated into three rakes and stowed on all three roads were sometimes accommodated when a special tour train moved between the two main islands. Of course in such a case, passengers would detrain prior to the consist being loaded aboard, since the public were not allowed on the rail deck.
Hope this helps with your understanding of how this process worked, at least in New Zealand.
Regards,