Well, this is actually a pretty good question which I also never actually thought of until now:
However I did figure out my opinion on it: She´ll represent all three of those things.
Why do I think this? Well, as the name of the sereis states "Friendship is magic" magic and friendship belong together in the world of MLP. They are pretty much the same thing.
As for the the harmony; magic is one of the six elements of harmony so Twilight will already be in control over one part of harmony and all of the elements of harmony are connected to one another by friendship. Without the friendship between Twilight and Rainbow Dash, Fluttershy, Rarity, Pinkie Pie and Applejack the elements wouldn´t work. So, I believe that all three things are connected to one another and can´t be seperated.