"Robert E. Lee's Headquarters Flag"
 
 
Generals had the most dangerous rank during The War Between The States. They were killed in a larger percentage than the men under them. "You can't lead from behind" was a common observation. While generals often lead their men directly from the front line, it clearly was not to an army's benefit that its very top commanders expose themselves to direct fire. They belonged where they could direct the overall movements of men.
Army commanders typically had, as HQ flags, the current national flag of the Confederacy. This went down at least to brigade level HQ's The adotption of the Second National flags did not mean the flag immediately appear in the field for HQ flags - as what was depicted in the "Gettysburg" movie. It was actually not until at least late October, 1863, before the first issued Second National HQ flags began to reach Lee's army. Most did not arrive until 1864. Until then the army used First Nationals as HQ flags.Lee's flag has an unusual star arrangement that was supposedly designed by his wife Mary to reflect the Biblical Arch of the Covenant.
Lee's HQ Flag was adopted some 14 years ago as the personal Flag of the Commander-in-Chief / Commander General of the Military Order of the Stars and Bars, inasmuch as that individual is, by virtue of office, the sentimental successor to General Lee.