Our first clue that darkness is important in this book? It gets mentioned in the very first sentence, which reads, "In the city of Ember, the sky is always dark" (1.1). We're guessing they're not spending winter in Alaska, so we know straightaway that something's up.
And indeed, every time darkness pops into the book, it's when something is very not right. Take, for example, the moment when Lina is running home after Assignment Day:
When she came to Hafter Street, she slowed a little. This street was deep in shadow. Four of the streetlamps were out and had not been fixed… How could people find their way through the streets in the dark? (2.4)
So on the one hand, darkness is kinda normal in Ember. It's par for the course that the sky will never be bright and blue. And it's not odd at all that the lights go out every night—that's you're your regularly scheduled programming in Ember. But when darkness appears where and when it's not supposed to be, well that's a big symptom that something's up—and it's nothing good.
Of course, that sounds like a bit of a paradox. How can darkness to be both normal and abnormal for the citizens of Ember?
Easy—darkness is linked to the unknown. The citizens of Ember have no clue that they're living in an underground city. They just know that a reasonable amount of darkness is to be expected. But as soon as the darkness starts intruding in on their lives more and more, it indicates that something is wrong—there's stuff they don't know or understand, and that's what's threatening.
But we can't stop there, now can we? If we ask the always wise Clary, darkness is about more than just the unknown—it's about the people themselves:
There is so much darkness in Ember, Lina. It's not just outside, it's inside us, too. Everyone has some darkness inside. It's like a hungry creature. It wants and wants and wants with a terrible power. And the more you give it, the bigger and hungrier it gets. (13.8)
Let's break this down. On a symbolic level, Clary is saying that we all have hunger within us—a selfishness that won't be denied. And if we give in to that dark hunger, it grows. Take the mayor, for example. Once he got a taste of those delicious foods, he probably just couldn't help himself. And once he got a taste of his power to hoard those foods for himself, well, why would he ever bother sharing? That hunger is a darkness because it leads to bad things. The more he hoards power and supplies, the more the citizens of Ember suffer, and the more likely it is they'll end up in literal darkness—permanently.
It doesn't seem like Clary is saying darkness is necessarily a bad thing; after all, we all have some inside of us, so it must be natural. But letting your darkness get out of hand is what leads to imbalance and problems. Letting your darkness have power over you… well, we've all seen Star Wars, so we know where that path leads. Unless your life goal is to be a Sith lord, we don't recommend it.
So keep an eye out for darkness, whether it's internal or external. Darkness isn't inherently evil, but too much of it is usually a bad sign.