There was a certain hierarchy on board of a Pirate Republic ship, to determine the most important functions and the line of command:

Captain:
The captain of a Pirate Republic ship has to possess the qualities of leadership, courage and generally chosen for his daring and dominating character. A Pirate Captain often was admired for his cruelty and destructiveness. A captain's power was absolute in time of chase or action, and he could discipline anyone who disobeyed his orders. He also had life and death power over anyone taken prisoner.

Quartermaster: (First or Executive Officer)
The quartermaster came next after the captain in exercising authority over the pirate crew; he was in charge of the men when the ship was not in action. He could punish the men for insubordination and arbitrated minor disputes among the men. The quartermaster usually led the attack and was the first to board the vessel. He was also in charge of food and water supplies. The quartermaster also assisted in numerous tasks, including attending to the binnacle (box housing the compass), steering the ship, and navigational duties.

Boatswain: (Chief Operations Officer)
The boatswain supervised the maintenance of the vessel and its supplies of naval stores (tar, pitch and tallow, spare sails, etc.). He was responsible for inspecting ships, sails and rigging each morning, and reporting their state to the captain. The boatswain was also in charge of all deck activities, including weighing and dropping anchor, and handling of the sails.

Ship's Master (Pilot): (Senior Helmsman)
The ship's master was an officer responsible for the sailing of the ship. He had to be a specialist in navigation and pilotage. He directed the course and provides himself with maps and instruments necessary for navigation.

Sailing Master: (Senior Navigator)
The sailing master was in charge of navigation. Of course, since charts were often inaccurate or nonexistent, his job was a difficult one. Many sailing masters had been forced into pirate service.

Master Gunner: (Chief Security Officer)
The master gunner was responsible for the ship's guns and ammunition. This included sifting the powder to keep it dry and prevent it from separating, insuring the cannon balls were kept free of rust, and all weapons were kept in good repair.

Carpenter: (Chief Engineering Officer)
The Carpenter was responsible for the maintenance and repair of the hull, masts and yards. He worked under the direction of the ship's master and was looking after the main tack and bowlines, or working the forecastle with the mate. The carpenter has no command and could not give an order even to the smallest boy; yet he was a privileged person.

Alchemist: (Chief Science Officer)

Surgeon: (Chief Medical Officer)
The Surgeon was responsible for inspections to judge the fitness of the new recruits, and treatment of the sick and wounded. While the owner of the ship had to provide the surgeon with drugs, medicaments, and other things necessary for treating sick persons during the voyage, the surgeon provided the instruments of his profession. The surgeon was not allowed to leave the vessel in which he was engaged, before the voyage was accomplished.

Mate: (Chief of the Boat – Highest Ranking NCO)
The Mate took care of the fitting out of the vessel, and examined whether it is sufficiently provided with ropes, pulleys, sails, and all other rigging necessary for the voyage. At the departure he took care of hoisting the anchor, and during the voyage he checked the tackle once a day. If he observed anything amiss, he acquainted the ship's master. Arriving at a tort, the mate caused the cables and anchors to be repaired, and took care of the management of the sails, yards and mooring of the ship. In case of absence or sickness of the ship's master, the mate commanded in his place.

The Pirate Republic’s Stronghold coverage area is currently divided via World Time Zones and the Equator. If an area constitutes the need for an additional Stronghold, the Pirate Republic Council will appoint a worthy member of that zone for approval of the Pirate Dread King. Either Navy or Marine members of the Pirate Republic may command Strongholds.

A Stronghold command uses the following positions:

Captain
Quartermaster
Boatswain
Master Gunner
Carpenter
Alchemist
Surgeon
Mate

Also includes any Warrant Officer and Enlisted Positions as well.

The Pirate Republic Royal Guard: (SEALS, Special Forces or Marine Expeditionary Forces)

The Pirate Republic Royal Guard is the Dread Pirate King’s personal guard. The PRRG have there own Ships and answer solely to the Pirate Republic King. PRRG members can be members of regular Pirate Republic Ships and have standard duties on that ship unless someone violates the rules of the PR.

Members of the PRRG can also be used as training officers of new Pirate Republic Ships or Strongholds.

The PRRG are also the Dread Pirate King’s emissaries in Stronghold Regions. PRRG appointments are the sole choice of the Dread Pirate King. 

A member of the PRRG keeps their current PR rank and adds their PRRG title to the end of their Rank/Name. Example: Pirate Captain Kidd of the Pirate Republic Royal Guard or PRRG.

Captain of The Pirate Republic Royal Guard - The commander of this particular division. 
Lieutenant of The Pirate Republic Royal Guard - This person is second in command. 
Royal Guard - These are the bulk of this guard type. They are the elite of the regular forces and can be of any profession. 

Knights of the Pirate Republic Council

The Knights of the Pirate Republic Council are the enforcement arm of the Council and Council members. The Knights are usually based at Strongholds or with their Council member benefactor. On rare occasions members of the Knights can be members of regular Pirate Republic Ships and have standard duties on that ship until they are recalled to the Council.

Members of the Knights are allowed Squires with the approval of the Council. A Knight with a Squire is responsible for the actions of the Squire. Knights also can be used as training officers at Strongholds.

A Knight can come from either the Naval or Marine Branches of the Pirate Republic. Knights are usually used as Master Gunners or Marine Chiefs of Strongholds. Knighthood appointments are the sole choice of the Council. 

Members of the Knights keep their current PR rank and add their title to the front of their Rank/Name. Example: Captain Kidd to Sir Captain Kidd of the Council Knights.

Captain of the Pirate Republic Council Knights - Commander of the knights. 
Lieutenant of the Pirate Republic Council Knights – This person is second in command.
Knight Commander - Command divisions of troops, command a certain order. 
Knight - The bulk of the force. 
Squire - These people are knights in training. 

Section 31

Covert Operations Unit. Duties are Classified.