One spin off from our war experiences of WWII was the need to train every man, every leadership job, so that say a Squad Lead is killed, one of the Corporals or Buck Sergeants can move right into that position without losing a beat. I know from my time at the Infantry School, we taught that lesson from the Basic Trainee up to the Officer Advanced class. We also used that same doctrine when instructing foreign students (School of the Americas for instance.)
Today's military plans for 40-50 different scenarios of every action. When reading about military command prior to the 20th Century, I find a distinct lack of scenario planning. When looking at the differences, I see that we sometimes get so far into the weeds today, we miss the really big tree on an open plain, but for the life of me, cannot understand how Commanders of yore would not put some rudimentary effort into planning for a few contingencies, especially considering the lead from the front style of leadership of the day.
One reason could be the exceptional growth of the Staff. When my son was in Afghanistan, he spent some time in the S3 shop as the Major's deputy prior to being assigned as the liaison officer to the Afghan Army. He reported that the Squadron S3 had a staff of about 40 men. I laughed when I heard that, the entire S shop (S1-6) for a Regiment had about 40 men when I was in the Army.
During WWII, Gen Eisenhower had a staff of 16,000 men to plan Operation Overlord, which in addition to effectively launching 12,000 aircraft, 7,000 vessels, landing 24,000 paratroopers and 160,000 men landing on the beaches, had to plan the logistics, the docks, piers refueling issues and the campaign of subterfuge in getting the Germans to believe they were hitting a different area.
To put it into simple terms, had Ike been in Afghanistan in 2009, planning an invasion with roughly 180,000 men, using the modern S Shop numbers, his S3 section alone would have consisted of about 32,000 men
I have not looked into the staff numbers during the Civil War specifically, but would assume that General Officers had relatively small staffs, even at the Corps level. Going out on a limb here, I would suspect the Civil War staff for an Overlord sized force would probably be a few hundred staff officers, but probably would not reach more than a 1,000. One would think someone would have come up with a plan of succession in the event of death or long term separation from duty of Commanders.