The PHQ, besides being a marvel of architectural design with its arches and towers, was a floating base of operations that a squadron of local superheroes called home and outfitted with a forcefield bubble and a missile defense system. It was visible from pretty much any point on the Docks. The forcefield made everything seen through it look oversaturated, like a TV with bad picture settings.
The headquarters of the Protectorate East-North-East is a refitted oil rig of some sort that sits out in Brockton Bay. Noted for having a powerful forcefield and defense missiles that have never been used. Most likely a fully anchored sort of rig and attached to a concrete pad underwater for stability. Did not appear to be greatly affected by being ripped up during the Battle against Leviathan.