There were some protocols based on the hierarchy of rank. For example, a ship might be asked to strike their colors when recognizing a ship bearing someone of a higher station. Right of way becomes an issue at times when a ship of lesser 'station' must fall by the way side to allow a superior vessel to pass. William Kidd's ego was such that he sometimes did not follow these protocols of his day, often snubbing those whom he did not recognize as his 'superiors'.
Still, I don't know enough on the subject myself to offer many examples, apart from the little I have read, so I look forward to the information this thread may glean.