What do I mean by "structure"? I mean the story beats and the relation between them. Now, there's lots of structural issues that first-time viewers will not consciously note and that might not be all that important. For instance, our first scene with the white collar puppeteers (hereafter Admin) and they are talking about the future: both far future plans (Hadley is planning to have kids) and near future (Hadley invites Sitterson for a drink later). So these people who will later be revealed as dangerous monsters are also associated with the future. After all, they're doing this ritual to insure the future happens. This might not make a big impression at first, but will come back as text when the Admins explain they are insuring the future.
Meanwhile, when we meet the kids who are being set up for the ritual, listen to their double-meaning dialogue, especially from Dana. She says things like "I knew what I was getting into" (when she's talking about her relationship with her professor--yet another way that adults fuck-over youth in this movie); and she says to Jules about the double-date nature of this trip that she's not going to have any fun "if you treat this like a set-up" (which is right but for the wrong reason). We may not notice the irony at first, but it's there.
As I said, those little echoes and ironies may not even be noticed at first; and while they may help the viewer subconsciously follow the story, we need stronger beats to keep the story moving. You know the Garth Marenghi joke: some writers use subtext, but they're pussies. We need some beats that viewers will notice and transitions that they'll be able to follow.
Naturally, since this is a movie in part about the voyeuristic pleasures of horror, many of those transitions are from the viewed subjects (the kids) to the viewers (the Admin) and back again. So we see the kids do something and the Admin respond and the kids react. This is a great lesson in screenwriting scenes: connect them not with "and then" but with "because." Many of the transitions occur by going through the camera, a technique that we've seen plenty of times, so much so that it's become transparent to us. But! Bonus: the fact that we see two separate story-lines play out that are separated by the camera/viewscreen means that we get a big surprise when the two story-lines combine into one seen--when we follow Sitterson on his last-minute dash through the tunnel and then he gets stabbed by Dana, viewers jump because we see worlds colliding. Also, how's that for a narrative hand-off: instead of Sitterson being the main character with the last chance to save the world, now we follow Dana.
We should note that "Sitterson runs to fix the problem" is something we've seen before, when he ran to blow up the tunnel (right after Amy Acker's character gives a Leia-esque "you guys are humanity's last hope!"). So the final Sitterson scene replays his triumphant heroism, but short-circuits it. Or if you want the motto form: set-up anticipation, deliver pay-off, frustrate / tweak anticipation.
(Also, is it just me or is there a motif of hands/arms running through this film: Curt says Holden has good hands; Patience Buckner talks about her good arm being hacked off; the giant arm at the end of the movie. What does that mean?)
And for another example of repetition and frustration, note that Dana and Holden have the same interaction with the one-way mirror in their rooms and the scary picture covering it up, which then leads to the frustration / tweak: the Admin isn't watching through the walls, but through a camera on the other side of the room. Or check out the Harbinger's two interactions: acting hick-scary with the kids and acting the same way with the Admin--only the other Admins treat him as a joke. Or (just one last one) the repeated "Let's get this party started" said by both the kids (really drinking and dancing) and the Admin (getting down to work and dancing poorly).
(There's another lesson here about letting your characters be competent in the way that Sitterson at the party understands something is wrong the moment before the phone rings; and another lesson in building anticipation in Hadley's long walk to the ringing phone.)
Now, from a three-act structure angle, we should note that the story is fairly straightforward for Dana: she has a turning point from Act I set-up to Act II danger in going down to the cellar where she chooses the diary; and then there's the Act II low-point when she realizes that Marty was right about there being puppeteers before seeing Holden murdered and being almost killed by a zombie herself.
But here's a question: can we say that the Admin storyline also has a protagonist?