The stated policy of the U.S. military in 1940 was that "Officers for Negro units might be Negro or white. They were to be assigned in 50 percent greater numbers than to similar types of white units. Negro officers were to be chosen and trained according to the same standards as white officers and, preferably, trained in the same schools. Negro officers were to serve only with Negro units and in overhead installations, and should command Negro troops only." (emphasis mine)

It wasn't until September 1940 that President Roosevelt ordered that all branches of the military establish black units - the Army Air Force had to that point staunchly refused to accept a single black trainee. To forestall black criticism over the official acceptance of segregation throughout the military, Colonel Benjamin O. Davis (the only black colonel in the U.S. military) was promoted to general a month later.

The lack of a sizable black officer cadre raised problems over the next two years; by the end of 1942 there were almost 470,000 black enlisted personnel, 10 percent of the military's total, but only 800 of 72,000 officers were black. Throughout the war, white officers commanded many black units; many black units also had white NCOs and trainers.

Given this situation, the problem of black officers commanding white subordinates seemed theoretical to many observers. However, it did occur: notably, during the reactivation of the 366th Infantry Regiment, which was formed under the command of Col. Edmund Andrews, a white officer. Four of the regiment's five other colonels were also white, but the fifth, West Hamilton, took command of the regiment in 1942 after Andrews fell ill. Hamilton remained in command throughout the war, and his regiment had the most integrated officer corps of any in the military.

While blacks were as a matter of policy not allowed to command whites, and segregation was meant to ensure this, the rank of any officer was, in theory, to be respected. White enlisted men were, in theory, required to salute and follow the orders of black officers. In practice, black officers often made a point of avoiding tense situations or ignoring slights. The following quote is from a letter to civil rights leader Adam Clayton Powell, Jr., from an anonymous black soldier (from Taps for a Jim Crow Army: Letters from Black Soldiers in World War II):

"On August 31st 1943, a white private told a Negro Officer who had reprimanded him for not observing the ordinary military courtesy of a salute, if you would take your clothes off and lay them on the ground I would salute them but I wouldn't salute anything that looks like you. The Officer called a Captain and told him of the incident. In the presence of the private, the Captain said, "Well Lieutenant, what do you want me to do about it?" The Officer reported the matter to the major under whom he was serving immediately. The Major advised "I wouldn't make an issue of the incident if I were you." The Officer insisted on preferring a charge against the soldier. He was transferred from the post three days later."

You might also check out:

-The Right to Fight: A History of African Americans in the Military by Gerald Astor.

-Strength for the Fight: A History of Black Americans in the Military by Bernald Nalty. Dryer but more detail than Astor.

-The Invisible Soldier, edited by Mary Penick Motley. Great oral histories.

-The Employment of Negro Troops, by Ulysses Lee. Old but free online and lots of meaty numbers.

EDIT: corrected a couple of typos.

Read "Black Armor" written by the White Commander of the Sherman unit. He talks about what the 'real situation' was for these men. It was hard as hell for him to get any of his men promoted to officers, they had more NCO's that Commissioned Officers. Yet they were one of the highest decorated tank units during WWII. They were also one of the most disposable Tank unites as well, often sent into no win situations. The Man that wrote this book talks about his Prejudice and how the reality changed it to respect for the men under him, and the anger of how the US Army treated him. There was even a quote from Patton cussing out Eisenhower for refusing assistance to the tank unit when they were sent into an ambush, and how Patton refused orders and sent in assistance to help them. Military rules did say one thing, but not many followed it, and a deft eye looked over this fact as well. But then, it did lay the ground work to get them better treatment and respect later on.

In what army?