What does it mean that the devil is lord over the flies? Who do the flies represent?
I'm not sure if I understand your question, but I'll do the best to interpret what I think you're asking. The Lord of the Flies itself (i.e., the pig head atop the stick) has many interpretations. A common one is that inside all humans is the capacity of evildoing (perhaps your "devil" reference?). The "Flies" might mean human beings. The "Lord" might mean the strongest impulse within humanity (i.e., evil). Throughout the story, this realization slowly occurs to the characters in the story and to the reader.
It takes a character with a certain insight (Simon) to see/recognize this reality. Once he experiences his epiphany and attempts to enlighten the others, like so many visionaries, he is destroyed. Along with him, there's the potential for his insight to be either misinterpreted or used for a greater good.
As the story ends, the reader is left to ponder which direction will be taken by the characters.