Hi borntoship,
If you are speaking of regular missions, the mission creator sets the number of containers to be transferred at each waypoint; the player has no control over the number transferred.
An exception is the Container Crane. It starts the mission with a certain number of containers on the dock—determined by the creator. The crane is like a player ship in that it has a single waypoint—on Vermaas—and that waypoint is completed when all of the dock containers have been loaded. There is no way to add more containers to the dock within the mission.
It is not necessary for the crane to load all the containers at once. Vermaas can depart with a partial load and return for the rest.
The crane cannot unload a vessel.
The crane can actually be used to load containers onto Sherpa, but the mission completion logic was not designed for that.
None of this helps much for a virtual shipping operation in multi-play.
The limits to container operations are explained in the Mission Editor tutorial, which you can download here:
http://www.shipsim.com/ShipSimForum/index.php/topic,2886.0.html (http://www.shipsim.com/ShipSimForum/index.php/topic,2886.0.html)
Regards,
Marty