I see it working like this, you use the map to plot your course,
Auto Launch takes you out, then hands over to super cruise assist,
SCA takes you out of mass lock, brings you to bear on the first jump target,
then hands over to FSD, and you jump,
then SCA brings you to bear on 2nd jump target,
Fuel scoop and honk on auto, as you orbit around the star toward 2nd target, then hand over to FSD,
and jump, until you reach your destination, however many jumps are within your fuel limit.
You can stop, pause and restart toward the next star anytime prior to jump, allowing for other actions,
or a complete change of direction.
Any emergency will put you into normal space, after a 5-30 secs Warning with Info, to deal with it.
Allowing time to take manual control of the ship.