I also found transport confusing. Ferry is quite clear, but unfortunately it's buggy, units inside the circle sometimes (most of the time?) are not being picked up. Embark and disembark are unintuitive.
The best way for me would be to have a command to issue both embark and disembark command with a single button, and treat all contiguous commands as movement for transport between load and unload.
units in point A, move command in point B, then click on "airlift" command, then click on C and on D, then attackmove command on point E.
What it should happen: units move from A to B, there they wait for transport; they are loaded, the transport move them on C and on D, unload them on D. Units unloaded then follow the attackmove order to E.
That's the most intuitive way IMO.
Most of the time I just want a bunch of units transported. Now I think I can get that done by issuing a move order and then pressing Embark... but I didn't get that when I was playing the transport mission of the campaign. That button is too much different in behaviour than the other commands.