The POW/MIA flag, like all others, must fly below the American flag.
The black and white flag representing America’s prisoners of war and people declared missing in action is the only flag the U.S. government flies with the American flag at the U.S. Capitol Rotunda. The flag’s history began in 1971 when the wife of an MIA soldier saw a newspaper story that inspired her to push for a flag honoring POWs and MIAs. The POW/MIA flag went up for the first time in the U.S. in 1989 at the Capitol Rotunda. Since then, like with the American flag, etiquette and rules have emerged regarding how, where and when the POW/MIA flag should fly.
With the American Flag
There are no codes requiring the POW/MIA flag to fly on the same pole as the American flag, but if it does, the POW/MIA flag needs to be lower. The Flag Guys say some people believe the POW/MIA flag should also be smaller, but there is no code directly related to size. The Advocacy and Intelligence Index for POWs-MIAs Archives says the POW/MIA flag usually should only fly with the American flag.
With State Flags
The American flag should be the only other flag on the same pole as the POW/MIA flag, but state flags can fly on other poles, according to etiquette. The armed forces have regulations, which don’t directly apply to civilians, about putting state flags ahead of flags for military branches, but they have no specific rules for POW/MIA flags. State attorney generals can set their own precedents for state flags.
With Military Flags
Flag etiquette code does not state specific rules for how POW/MIA flags should fly in relation to military branch flags, such as the Navy flag. The choice is left to the person or organization flying the flags. The Flag Guys recommend the following order: U.S. flag, military flag, POW/MIA flag.
According to the United States Flag Store, if there is one flag pole, the POW/MIA flag should go directly below the American flag; if there are two poles, the POW-MIA would stay below the American flag and state and other flags would fly on the second pole. If there are three poles, the POW-MIA flag should fly in the middle with the American flag on the right pole and all other flags on the left.
There are certain American holidays and days of honor on which the POW/MIA should specifically be flown, including Independence Day, Memorial Day, Veteran’s Day, Armed Forces Day, Flag Day, and National POW/MIA Recognition Day.