Let's get the easy part out of the way first: "the Lord of the Flies" is what Simon ends up calling the severed pig's head—presumably because it's covered in flies. So, calling the book Lord of the Flies brings the boys' primitive violence front and center.
Now let's break it down. "Lord" is a word of power, and the desire for power drives the book's central conflict: who gets to decide what the boys will do? "Flies," on the other hand, connote death and decay. Put them together, and you've got death and decay tied up with power and corruption. Nice.
Lastly, as if that weren't enough, "The Lord of the Flies" is also the popular translation of Beelzebub, who's either a demon or the devil himself, depending on how you like your mythology. And that makes us ask: is evil external to us, like a talking, decaying pig head? Or does Simon call the head "Lord of the Flies" because he sees it as a manifestation of the boys' nature—and possibly his own?