I think that the collage of whispers is basicly the Mages guild without imperial charters and batle mages. They work for themselves, and don't fight for any empire. kind of like a magical school version of the red cross. But the Synod would be a group dedicated to using magical abilities to serve the emperor. Kindo of like a magical version of the blades/whatever Titus renamed them to be.
Speaking of battle mages, wonder if there's been any changes to that organization post Titus Mede...I may have overlooked references in the novel. Was kinda speed-reading to keep up with the ones who got it before me. Need to go back and read it again, and soak it in more.
I always assumed the Imperial Battle-college was separate from the Legions and the Mages Guild.