Some thoughts:

Hardee’s Tactics

The manual is titled Hardee’s Rifle and Light Infantry Tactics, For the Instructions, Exercises and Manoeuvres of Riflemen and Light Infantry, including School of the Soldier and School of the Company, by Brevet Lieut W. J. Hardee. 1855

As such, I consider it a guide to parade ground training and dress parade protocol. This was published prior to the war and Captain’s date of rank in the old army had meaning, real and imagined. Peace time duty was rather static with little change in personnel occurring,

Just musing, I would believe the line of march would dictate the placement on the combat line. And this order dependent on how the companies wheeled into column from their parade ground muster line. Further, I would believe companies would form up in line in accordance with their Alpha designation. And then, the Regimental commander may have pre-planned company placement sometime in advance.

I would think the number of companies on the line during combat would depend on the ground allocated. Furthermore, I believe it was common to place companies in reserve and on the skirmish line, for example, see: http://thomaslegion.net/unionandconfederatearmyorganizationsatthebattleoffirstbullrun.html Here experience may have dictated these choices.

Civil War Confederate units were formed from the civilian populace rather fast from various locals and formed into 10 company regiments at some convenient gathering place. I suspect that company designations were assigned as individual companies arrived.

Here is one example. Date of rank as we know it in the old army has no meaning in the way they were formed. Some may have had prior service, i.e. Mexican, Indian wars, militia, etc. These Alpha designations did not change during the war.

43rd Tennessee Infantry
[5th East Tennessee Volunteers]

Their company designations most likely occurred upon arriving at Knoxville.

Company A Called into service at Hiwassee Mines, Tenn., October 19, 1861

Goodman, John, Captain, Co. A, age 40, enlisted October 19, 1861

Company B Called into service at Sulphur Springs, Tenn., October 16, 1861

Cawood, Andrew J., Capt., Co. B, age 36, enlisted October 16, 1861

Company C Called into service at Pikeville, Tenn., October 26, 1861
Hill, William J., Capt., Co. C., age 34 enlisted October 26, 1861

Company D Called into service at Decatur, Tenn., November 1, 1861

Hodge, Ambrose W., Capt., Co. D, age 38, Physician, enlisted November 1, 1861

Company E Called into service at Rogersville, Tenn., November 5, 1861

Phillips, John W., Capt., Co. E, age 34, enlisted November 5, 1861

Company F Called into service at Roane Co., Tenn., November 9, 1861
Turner, Sterling Tally, Capt., Co. F, enlisted November 9, 1861

Company G Called into service at Mossy Creek, Tenn., October 19, 1861
Neff, David Tennessee., Capt., Co. G, age 52, enlisted October 19, 1861

Company H Called into service at Riceville, McMinn County, Tenn., November 16, 1861
Lafferty, William L., Capt., Co. H., born October 15, 1822, enlisted November 16, 1861

Company I Called into service at Charleston, Tenn., November 13, 1861

McKamy, William H., Maj., Co. I, enlisted November 13, 1861

Company K Called into service at Ooltewah, Tenn., October 17, 1861
Aiken, Jasper Newton, Capt., Co. K, enlisted, October 17, 1861, elected Capt. December 14, 1861