Let's break this down.
First we'll look at the rules for Advantage/Disadvantage:
Sometimes a special ability or spell tells you that you have advantage or disadvantage on an ability check, a saving throw, or an attack roll.
Advantage only applies to one ability check, saving throw, or attack roll.
In the case of Scorching Ray:
Make a ranged spell attack for each ray.
there are three separate attack rolls happening (one for each ray). Therefore, Advantage would only apply to one of those attack rolls for one of the rays, not all of them, regardless of whether they all hit a single creature at the same time or separate creatures.
In the case of attacking a creature within the area of Faerie Fire (as you use as an example), all three attack rolls would have Advantage solely because of the wording of Faerie Fire:
Any attack roll against an affected creature or object has advantage...
Scorching Ray's instantaneous duration has no effect on Advantage/Disadvantage though, as that only refers to the length of time the spell persists (see page 203 of the PHB).