A ferry is set up when a transport is specifically instructed to move along a certain waypath, designated by the ferry icon. A transport with a ferry associated with it will move land-based units from the starting point to the final drop point of the path. At that point, the ferry will return to the starting point by retracing its initial path.
To set up a ferry route, move a transport aircraft to the point where you would like the route to begin, and select the ferry command. While holding shift, click the ground to create a series of waypoints. The last waypoint will be the ferry's drop off point.
Once you have set the first waypoint, a ferry icon should appear on the ground beneath your transport aircraft. It will remain there until the transport is assigned to another task or destroyed. To order units to board the ferry, select them and then right click on this icon as if issuing a move command. Optionally, you may set this icon as the rally point for one or more factories, and new units will automatically be ferried to the end of the route.
You may assign additional transports to the route by ordering them to assist the transport used to create the route. Select the additional transports, and right click the original ferry transport.