The Alchemyst Theme of Good Versus Evil

A fantasy novel wouldn't be complete without a fight between good and evil, now would it? In The Alchemyst evil takes the form of the powers of darkness—the "Dark Elders" who want to reclaim the earth and their minions—cats, rats, and crows. "Good" is much more colorful, but it's also a whole lot more ambiguous. Flamel and Perenelle assure their crew that they battle against evil, but sometimes their choices seem a little, well, unclear. But if their auras—their "magical footprints"—are any indication, we'll take the pepperminty goodness of Nicholas Flamel over Dee's rotten eggs any day.

1. Does Nicholas Flamel represent good, and Dr. John Dee evil? Is it really that simple? Take a look at the scene in which Dee tries to tempt Josh. And what about the scene in which Flamel first meets Dee. Given what we know about the Elder Race, can we really know for sure who's on the good side and who's on the bad side? 
2. Who are the "good" characters, and who are the "bad"? Are there some that don't fit into either category?
3. Are Josh and Sophie good? Evil? Do they perhaps have both of those qualities in them?