It was indeed the customary mode of organization for infantry in 1861 to have flank companies, and where available to have one or both armed with rifles potentially. In any case it was presumed that at least the flank companies (generally companies A and B, the two most senior of a given outfit by rank of captains generally) of a regiment or battalion with muskets might train specifically as light infantry when required; and that the left flank company particularly might be designated for rifles.
From Scott's Infantry tactics, 1861 edition, on the organization of an infantry battalion. and relative to flank or light companies...
After the mid-1850s the rifle and light infantry companies drilled by Hardee's light infantry and rifle tactics. In that drill there is no particular distinction relative to flank companies and battalion companies, as they are all drilled by the same light infantry and rifle system, irrespective of arms in hand...
The result being any companies or whole regiments/battalions employing this system would be deployed as skirmishers when required.
That said, a battalion commander employing these tactics would still likely have preferred any rifle companies for skirmishing potentially, and where only a part of the battalion was required for skirmishing, it remained most convenient to deploy the flank companies, so as to least disorder the balance of the line.
Ross Brooks notes that it is evident that most of Wheat's battalion in 1861-62 had muskets, and the Tiger Rifles certainly armed with M1841 Harper's Ferry Rifles, but he suggests at least one other company likely had rifles too considering a large quantity of rifle ammunition drawn, etc. Considering the Tiger Rifles were the battalion's Company B, it would appear that it was the left flank company in the primitive organization of the battalion.
The troops employing Hardee's system generally so formed, with Co. B on the left flank in their primitive or original formation.
Some period example...
Relative to Wheat's Battalion Mr. Shreckengost on p. 46 suggests the battalion at Camp Moore would have been instructed in the "heavy infantry" and the "light infantry" tactics. If he means by this that they drilled by other than Hardee's rifle and light infantry tactics (as if learning both Scott's infantry and Hardee's light infantry/rifle) he is certainly mistaken. The volunteers and militia in Louisiana were principally instructed by Hardee's Tactics, as they had been established as the standard for all Louisiana foot troops by the Military board at the close of 1860...
...
Shortly after, even the fire companies of New Orleans were engaged in drilling by Hardee's tactics or light infantry and riflemen...
From May, 1861...
The Confederate reprints of Hardee's in 1861 on were revised, considering that the former "light infantry" tactics were now practically standard for all infantry, they were then referred to as "infantry and rifle" tactics.
There was no lack of copies of Hardee's tactics available. Here a girl's school employed a copy to exercise the young ladies...
Regarding the fighting at Manassas...
N.G. Evans, who commanded the brigade to which the battalion was a part at First Manassas, reported of their action on the field as follows... initially with one of Wheat's companies as skirmishers...
Wheat reported that before contact at Manassas he indeed deployed Company B, the Tiger rifles, as skirmishers, and also Company D, the Catahoula Guerrillas. It reads to the effect of these skirmishers engaging those of the enemy at length, and Wheat wounded on advancing the balance of his battalion... His official report can be read here:
Supplemental Report Report of Major Chatham Roberdeau Wheat, First Special Battalion Louisiana Volunteers SUPPLEMENT TO THE O.R. – VOL.1: REPORTS ADDENDUM TO SERIES I, VOL. 2, pp 194-195 Manassas, …
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Brigade Commander Evans again...
In the subsequent history of the battalion there were apparently occasions when the whole outfit was deployed as skirmishers, etc.
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