Without additional information, I'd probably install the Unity in Site A, where your CCM cluster resides. This is more for management than for performance. With an OC-12 between sites, performance should not be an issue. If the connectivity does break between sites, Unity and CM can continue to work together. I believe that Unity for Domino will still work when Domino is offline and re-sync like it does with Exchange. Keeping the servers together will make upgrades/maintenance easier as well.
