Ken,
My response is based on my limited knowledge of the military organization of a regiment not the 40th Regt. in particular. I have based my information on Company C being usually in the center of the formation. Was that from "Hardee's Tactics" or some other military instruction manual?... I don't know.

I do know that I have seen the layout of a regimental formation that showed the order of companies in various military formations; can't pull it up from the hard drive in the hard head.

My main reference is the 7th Regt. Miss. Inf. in which the Color Company was company C "Amite Rifles" when the regiment was organized, and retained that position throughout the war.