You need some transports beforehand. Valkyries work best. Surfboard probably works but it is a terrible unit that needs to die in a fire, I don't recommend using it regardless.
You choose the ferry route "command" (not really a command, it's available even without any units selected) and click a source and a destination point.
Now, any units' move orders into the source circle are handled differently. On arrival they get a Wait command and an idle transport moves them to the destination, whereupon they continue with their queue. If no transport is available they patiently wait.
One use case is to speed up arrival from factory onto the frontline. It is unused because facs are dirt cheap so it's better to make a new one on the front instead unless you have spare transports from elsewhere.
The other use case would be to create an automated bridge of sorts between impassable areas. It is unused because on maps with such areas (eg. water) there is absolutely no reason not to use the fac that can traverse it by itself (eg. amph).