The Red Pyramid refers to Set's giant pyramid constructed by demons in Phoenix, Arizona. The thing is basically a massive time bomb: at sunrise on Set's birthday, it'll explode, taking a good chunk of North America along with it. Better yet, Set plans on entombing Osiris—and later, the other gods, if he can get his hands on them—inside the pyramid, so that their energy will fuel an even bigger explosion.
The title takes on additional significance when we realize that Apophis, the primal force of chaos, was manipulating Set into wrangling enough destruction to release it from its prison. Set digs destruction and all, but he wants to be king, which means he has to have someone to rule over. There's not much for a king to do if all he's got is a gigantic wasteland.
By the time they get to the climactic battle that ends the book, Sadie and Carter have figured out that Set's a bad guy—but not the biggest or baddest bad guy in the book. That distinction goes to Apophis, who masterminded the whole red pyramid thing. It makes sense, then, that the book's plot and title both emphasize layers of deception caused by chaos. Chaos is the real enemy here.