In the interest of ruling things consistently, this is to elaborate on how exactly Scale works, in terms of a Spell Factor.
As shown in the table below, Scale breaks down into three categories: Number of Subjects, Size of largest Subject, and Area of Effect.
When constructing the Imago for a spell, the relevant aspect that determines whether Area of Effect is used or not is (essentially) how precise you wish for the spell to be.
The simplest case is targeting a specific number of Subjects, and is fairly straightforward:
For example, targeting a specific quantity of Subjects, even if that quantity is just one, the first two columns (Number of Subjects and Size of largest Subject) are what is used. For example, targeting five people with a blessing, the largest of which is Size 6, would require either a -6 on Standard Scale (which allows for up to 8 Subjects, each up to Size 8) or a -2 on Advanced Scale (which allows for up to 10 Subjects, each up to Size 10). One thing of note, is that a spell that has multiple Subjects is still only one spell, so if it is dispelled on one target, it is dispelled on all targets, as the Imago of the spell is unwoven once missing a piece, like tugging a loose thread on a sweater.
However, there are many situations that are more complex than the above scenario that determine whether Area of Effect is used versus Number/Size of Subjects. Ultimately it depends whether you are affecting a specific area, or a specific target. To affect an area it must easily definable, and if mobile, it must have an external (to the spell) frame of reference. Valid areas would include "blessing everyone on the deck of this ship" (-8 Standard Scale, -0 Advanced Scale), "igniting a five-foot diameter sphere where ever this bead of flame, that I throw, lands" (throwing a spell, -0 Standard Scale), and "everyone within fifteen feet of me is invisible" (-2 Standard Scale). Generally speaking, Areas of Effect are not selective, mobile, or have complex shapes, so using the above examples: if an enemy boards your vessel, they are also blessed; if you misaim the bead of flame and it lands next to an ally, they get hit by the five foot sphere; if an enemy closes to melee range with you while you are surrounded by your sphere of invisibility, they also turn invisible.
With ongoing Area of Effect spells, potential subjects may move in and out of them, each of them being affected by Withstand separately. For spells that have a specific number of "charges", such as Exceptional Luck, the charges are shared among all active subjects.
In order for an Area of Effect to be selective, the Subjects/Area to be excluded must have Warding Gesture (Fate ••) cast upon it. If the mage who cast Warding Gesture (Fate ••) is the one casting the Area of Effect Spell, they can choose to exclude any valid Subject. If Warding Gesture (Fate ••) had the +2 Reach option, it will Clash with any supernatural effects that have an Area of Effect.
In order for an Area of Effect to be mobile, and not just "anchored" to a single point in space, it must have an external (to the spell) frame of reference. This is why an Area of Effect centered on the mainmast of a ship will move along with the ship, but a spell targeting a point in the air two hundred feet up will not. The frame of reference must be part of, or connected to, the spell's Area of Effect - in order to affect a point in the air two hundred feet above the ship that moves with the ship, the Area of Effect must include at least part of the ship, such as a cone whose point is resting at the top of the mainmast. As described above, subjects may move out of the Area of Effect, which can potentially have unintended side-effects if the spell is particularly dramatic. For example, an Area of Effect Regeneration (Mage 2E Core, p. 152) will only stay active while in the Area of Effect - leaving means the regrown flesh rapidly withers away into nothingness.
By default, an Area of Effect has an easily imaginable shape, such simple geometric shapes: spheres, cubes, cylinders, etc... In order to have a substantially more complicated shape, it must be tied to something external to the spell, much like making an Area of Effect mobile. This is why mages frequently have chalk or paint in their tool kit, as painting a maze on the floor would allow the mage to create a maze of invisible force walls. Drawing out the shape on the ground or other surface can be included as part of the ritual time for the Runes Yantra, and if it takes longer than the runes normally would (due to the size or complexity of the shape being drawn), there is no additional time spent for using the Runes Yantra. This drawing need not be readily visible (such as throwing a carpet over it or building a second, false floor over it), but it must exist, and mage must knowingly incorporate it into the Imago of the spell.
As an example of the above, lets assume that Petey the Pirate-Mage wants to cloak his ship with an Invisibility (Mage 2E Core, p. 143) spell. As a new Obrimos, just freshly Awakened, he does not know the finer points of constructing an Imago, so he throws a big Invisibility spell (-2 Advanced Scale) in a sphere around the ship without thinking. Chaos immediate ensues as the ship turns invisible, as does the crew and some of the surrounding water; thankfully, the ship passes out a few minutes later, as the spell was not anchored to anything and there is now a hemisphere of missing water in the sea behind him.
Learning from the previous attempt and talking to his mentor in the company, Petey decides to tweak his Imago in two ways: one, tying it to the mainmast, so that it moves with the ship, and two, making it so the spell doesn't turn everything inside the Area of Effect invisible, but rather that everything inside the sphere is invisible to those outside it - this way, the crew can still see the ship and each other.
Satisfied this is working far better, the ship sails on its way, until passing near a ship of the Spanish Inquisition. Confident in his magic, they sail closer than they should when suddenly the Inquisition ship fires several loads of grapeshot in their direction! Assuming that the spell did not work for some reason, Petey decides that discretion is the better part of valor, and they turn away and Petey casts Velocity Control (Mage 2E Core, p. 145). Having been warned of this spell, he knows to not cast it as an Area of Effect, as while the ship would begin to move faster, so would water around them, bullets shot at them would rapidly accelerate, winds would grow chaotic, etc... He instead reaches out, and stretching himself to his absolute limit, casts it targeting the ship and the crew as a whole, casting at -8 Advanced Scale to affect up to 80 Subjects (more than enough for the crew and vessel), each up to Size 25 (it's a smaller ship, meant for speed, not power).
They rapidly zip away, and Petey talks again to his mentor who, while uncertain why the Inquisition would have noticed them (they certainly have no mages in their ranks), suggests that the Area of Effect was likely affecting things like the waves and birds so the Inquisition vessel probably noticed waves that would suddenly stop or start and birds that were appearing and disappearing as they passed through.
Contemplating how to handle this, Petey sails into Nassau and meets up with his old friend, Mikey the Mage-Pirate, who asks to join Petey's crew. Knowing that MIkey is a skilled Mastigos who has also dipped into Fate, Petey accepts, and the two set sail once more (after a few days of course). Petey, now rested and ready, casts his Invisibility once again, now augmented with guideline/runes painted over the ship and sails (the most obvious of which get bits of canvas stitched over, like a patch, to hide them) at different points, so that the Area of Effect (still -2 Advanced Scale) now is about 8 feet out from any surface of the ship, including the sails, using the same inside/outside distinction that he used before.
This works quite well (plus Petey doesn't tempt fate by sailing too close to any more Inquisition ships), though some of the crew complain, as from certain angles, parts of the ship disappear, due to flapping sails or gaps in the coverage - for example, one cannot see the crow's nest when standing next to figurehead at the fore of the ship. Hearing the complaints, Mikey offers a solution: he will cast Warding Gesture (Fate ••) on the crew to help out Petey. The two of the talk, and Mikey explains how to incorporate it into his casting of Invisibility so that the crew will be able to see the ship, but for the ship, and 8 feet out from any surface or sail, to be invisible.
Gathering the crew on the deck, Mikey casts Warding Gesture (Fate ••) on the crew (-4 Advanced Scale to target up to 20 Subjects), using all three Reach options and a high Duration for maximum future-proofing, and then lets Petey know he is finished. Using what they have discussed, Petey casts Invisibility (-2 Advanced Scale), incorporating his runes for the specific Area of Effect and spending an extra point of Mana to use for the Warding Gesture (Fate ••).
Now, the crew is no longer unnerved, able to see the ship and each other (so long as they remain on the ship), and so long as everyone stays on the ship, or at least within 8 feet of it, they will remain invisible to those outside of the Area of Effect. Satisified, Petey thanks Mikey for his help, and the two of them sail off, embracing their newfound freedom of being quite difficult to spot.