Some years ago I did some research on how to fly flags and ensigns and signals. Previous to my research because of the "hippy movement" congress washed its hands and removed all laws pertaining to flying the American Flag. However, there are two main places where we get our flag culture--the U.S. Military which has many rules and orders and Chapman's who borrowed most of the rules and regulations from the military in 1917. I also went back further then the beginning of the United States and looked at Flag Etiquette in England and France, early sea powers. Essentially, you can fly any flag you want anywhere you want. I have friends who sail almost around the world (but got bored and come back to the northwest) and they flew a Swedish, Canadian and the U.S. Flag depending upon where they were and the response they might get. The flags are just signals telling others who you are (One of my friends was Swedish, his wife was Canadian and they sailed out of the U.S.)
Given all this, we do tack on a lot of traditions on our flags, look at some of our military flags with the abundance of battle ribbons attached--one can hardly hold up the flag because of the added weight. And the tradition of the sea is formable. At present most boats fly the American Flag off a staff at the stern of the boat. Some like to fly it three quarters up the backstay (except Hunters who don't have them) where the gaff of the main once flew years ago. Even then, skippers like to show their "colors."
In today's boats, we still follow a international tradition of flying the next important signal off the starboard shrouds because when ships of the line were tied up in port (on their port side) they wanted ships coming in to know who there were, what they were doing and in many cases, who owned the ship. Today most of us fly our yacht club burgee(s), the 12th man signal, USPS or USCG auxiliary burgees. I would think it would be honorable to fly the U.S. Marine Corp flag in this position. Your lesser valuable signals could be flown on the port side of your boat. Perhaps your martini flag?
In the process and looking up boating signals, I followed a thread on the Pirates Flag. As far as i could find, pirates didn't have a flag--they used a number of different national' flags to confuse the victim ship. But it appears that after WWII from movie sources the present day Pirates flag became popular and it's now flown for enjoyment (to indicate your mood?).
In summary (wouldn't you know an academic when you hear one?) you can fly any flag of importance to you from the any place that is easily seen by others, then fly your secondary important flag from the second most looked upon spot on your boat. For most of us that would be the stern and the starboard shrouds. Best wishes on your flag flying.
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