The penguins must have an HQ controlling their positions on the team and their ranks. The penguins rank is barely known, but info leaked into the public later. This page will compile the penguin ranks and if there are any new characters that are penguins, they will be added.
His rank has to be above the penguins seeing his apparent age, he may have the rank of colonel or major. And since Skipper told his full name including his rank which is Special Agent then he must be sent on special missions.