Both Johnston and Lee operated with divisions on the Peninsula (although that became loose terminology after Jackson and the "Valley Army" joined up for the Seven Days). Lee went to two "wings" in August.
This was because Army Corps were not authorised by law at the time. The Confederate Congress passed a law authorising army corps and the rank of lieutenant-general to command them on 18th September 1862 (two months after the Union authorised corps).
"The Congress of the Confederate States of America do enact, That the sixth section of the Act to provide for the public defence, approved on the sixth of March, eighteen hundred and sixty-one, be amended by adding after the words "brigades into divisions," the words "and divisions into army corps," and each army corps shall be commanded by a Lieutenant-General, to be appointed by the President, by and with the advice and consent of the Senate, who shall receive the pay of a Brigadier-General.
APPROVED Sept. 18, 1862."
Like in the Union, the power to create corps and appoint commanders was reserved for the President only.
The divisions of March 1862 were conventional, with typically 3 brigades. On the Warwick line Magruder had his army initially divided into normal sized divisions, but then Johnston reorganised the army into four wings of two divisions each, but at some point each of these wings is designated a division, despite still containing two divisions. To this the Army of the Appomattox (i.e. former Norfolk garrison), Army of the North and some divisions culled from the coast were added.
Despite having "divisions" the same size as Army Corps, and with multiple divisions within the division, the term corps was never used, because there was no legal basis for the formation of army corps, and the regulations (like US regulations in early 1862) set the division at the largest body below an army.
Now, in the West, each of the three numbered "corps" were an independent army (Army of the Mississippi, Army of Mobile and Army of Central Kentucky respectively). Arguably these were still legally three armies.
Similarly, once combined into one body Halleck called his three "armies" corps (Tennessee Army Corps, Ohio Army Corps and Mississippi Army Corps), and stripped a reserve out from the larger two, like Beauregard had. Interestingly, each of these "corps" was roughly the size of one of the pre-reorg Corps on the Peninsula.