It is important to remember that, unlike the Difference Engines, the Analytical Engine was always a work in progress for Babbage. It was constantly evolving, sometimes dramatically so, as he had new ideas or found better ways to solve old problems, and since he was not actively trying to construct it, he was uninhibited in making large scale changes.
Thus, to hold a meaningful descussion and come to a definitive conclusion on any particular subject or detail, it is usually necessary to specify which particlar version of the AE we are considering. Without this, the answer might be quite different, inconsistent, or even completely meaningless.
We generally refer to different versions by Babbage's own „Plan“ numbers, though dates can be useful markers too. Babbage drew large plan view drawings for each significant revision of the Engine. They show the layout of all the axes in the machine. In modern terms we might say they define the micro-architecture of that particular version. However, as stand alone documents they are not particularly useful since they give zero insight into how any of the resources were intended to be used. Any meaningful interpretation requires reference to the Notations. However, many of the plans were quite transitory as the Engine was evolving rapidly, and only in a few cases are there relatively complete Notations to accompany them. Plans 16, 25, and 28 stand out.
Plan 25 is particularly well known because Babbage had the plan drawing of this version engraved for publication. It dates from 1840, around the time Babbage presented the Engine in Turin and shortly before the time Lovelace was working on the translation and Notes, so it is probably closest to the version Menabrea was describing.
Babbage went on to make another very major revision though, before arriving at the (physically) simpler Plan 28 around 1843.
The most extensive analysis was done by Bromley, and summarised in a series of papers:
Bromley, A. G., „The Evolution of Babbage's Calculating Engines,“ Annals of the History of Computing, 9, 2, 113-136, 1987.
Bromley, A. G., „Charles Babbage's Analytical Engine, 1838,“ Annals of the History of Computing, 4, 3, 196-217, 1982. Reprinted in IEEE Annals of the History of Computing 20, 4, 29-45, 1998.
Bromley, A. G., „Babbage's Analytical Engine Plans 28 and 28a - The Programmer's Interface,“ IEEE Annals of the History of Computing, 22, 4, 5-19, 2000.