I'm not sure if they ever say in the manga, but is the Army of the Masks with Aizen? It seems as if Aizen's underlings are the Hollows who have been transformed, and the Vaizards (sp?) are the Shinigami who have been transformed.
The Arankaru's seem to want to kill Ichigo, while the Vaizards want to recruit him. It seems to me that they're two seperate factions.