The clue to how many flags Union or Confederate regiments carried can be found in the drill manuals that both sides used.

Hardee's Tactics, based entirely on French manuals, called only for one flag to be used. This was based on the French regiments (2-4 maneuver battalions) dropping battalion flags since the Napoleonic Wars and going with a single regimental flag. Thus, the US Army went with that for a time (after having two flags before which also were changed over time in terms of patterns). In 1861, the US Army Regulations added the second flag back (regimental color - blue with eagle painted/embroidered on the field and unit designation in the scroll below it) and Casey's Tactics, the Union drill manual, basically Hardee's redone (but Hardee was now a Confederate officer so the Army could no longer use his manual) also went with two flags.

Both manuals also called for flank markers; two per regiment for each of its flanks. Gilham's Tactics, used largely by militia, called for three flank markers, called guide flags. The third flag must have been with the regimental colonel with the other two on each flank. Guide flags had about as much importance with moving a regiment on the battlefield as did the unit colors but they get left out most of the time.

Hope this helps.

Greg Biggs