From the Army Regulations of 1857, there were no brigades or divisions in peacetime generally, unless required to be formed for combat purposes.
The only permanent legal organizations in the Regular Army before mid-1861 were staff and regimental.
Notice there is only one major-general, and three brigadier-generals before the war. Many of the officers held "brevets" besides their regular commissions. For example, the major General, Winfield Scott, held a brevet of lieutenant general. There were three brigadiers. Brig. Gen.s Wool and Twiggs held brevets of major general.
The Army was distributed among territorial Commands. These were the Departments of the East, West, Texas, New Mexico, Oregon, Utah, and California. When combat forces were organized within these departments, they were organized as was found best by the officers in command.
During 1861-65 the departmental boundaries changed, as necessary.
Where it was necessary to form brigades, the senior officer present, frequently acting under a brevet rank, would assume command.
Same with battalions. It was frequently the case that companies from several different regiments were combined to form battalions for field service where necessary. As brigades/divisions were not fixed by law, the terms were not always employed in the usual manner. For example, in the Utah war, Brevet Brigadier General A.S. Johnston (colonel of the 2nd US Cavalry Regiment), commanding the Dept. of Utah, formed his active force into three brigades which he called "divisions."
During the 1861-66 period the regular Army's territorial Department commands continued, though modified relative to the exigencies of the war. They continued after the war too. As did the general bar upon permanent brigades/divisions/corps. From Kautz's 1866 "Customs of the Service"