If I correctly recall, Gilham called for three marker flags whereas Hardee and Casey called for only two.
I have the flag portion of the Von Steuben manual and it only calls for two flags, just like the British Army of the Rev War period. I know that some units went with wing flags and could carry as many as three but that is not what the Blue Book called for.
In 1861 some CS units went into battle with their company colors, and in 1863 some of the combined CS regiments also fought with both banners of the combined regiments (as at Chickamauga). However, by 1864 this seems to have been shelved and in 1865 the CS War Department issued orders for combined regiments that stated they could only fight under one flag.
Greg Biggs