It was common practice for Instructions to be issued along with Letters of Marque to clarify the intent of the Letters for a particular endeavor. Few of them have survived

Anti Pirate Squadron Instructions 1627
Orders to the Admiral of the squadron to stop French pirates in 1627 England.

Capturing Pirates Instructions 1577
Detailed instructions for capturing pirates and sea rovers. This would accompany a Letter of Marque.

Henry Morgan’s Instructions 1670
One of the most interesting document in the collection. It spells out everything he is empowered to do; and he sure took it to the extreme. See also Morgan’s Letter of Marque

Enforcing Gun Salute Instructions 1673
Instructions for enforcing the gun salute and taking captured English seaman out of foreign ships.