Carlos is a Commandant within the Inquisition. As such, he oversees different operations, traveling to various locations to fulfill his duties.
At the beginning of the game, Commandant Carlos is found at the Crystal Fortress, where the Nameless Hero is also posted. Although a high-ranking Inquisition officer, he is willing to override orders if he feels a course of action may be a threat to the safety of citizens of the Empire. This is demonstrated when he orders the Nameless Hero to acquire all of the titan artifacts and use them to fight Mara, rather than to hand them over for delivery to the Water Titan in an act of alliance.
The Son of Steelbeard does not encounter the Commandant until he reaches Fog Island. It appears the Inquisition has recently started settling and exploring the island to determine its possible strategic importance and habitability for citizens of the Empire. Carlos is there to oversee the mission and strengthen his men against the influence of the Shadows.