Hello Herr K,
There's a bug on how this works at the moment, unfortunately. AI was found abusing the load features by doing some, let us say imaginative things, so that was fixed, but as a side effect the Boat/Ferry load to Engineering Trucks was broken.
When it is all working as supposed again, you should have these two options:
Engineering Trucks to Ferries
A Pontoon Ferry at a Shallow Water hex, you can drive the Engineering Truck there, and load it onto Ferry for crossing.
Ferry already carries all other types of vehicles
Ferries to Engineering Trucks
Here the process is as follows:
Engineer Platoon loads into Ferry (or Crewed Boat) to mimic the loading procedure.
Ferry (or Crewed Boat), having the Engineers loaded in, Loads onto Ferry, Ferry ends on Engineering Truck, Engineer Platoon end up unloaded in the same hex.
So you can load vehicles to Ferries without Engineers, but you cannot load Ferries to their transports without the manpower, that's what the process depicts.
It is broken at the moment, to be fixed on a future UPDATE, maybe already 2.01.