Isn't it kind of circular logic? The 12 element army is in theory derived from 'normal' forces in battles actually fought. So applying it to a specific battle in time should be easy if the list is good. So doing that for each army would be the first step.
Actual battles do have specific terrain and other factors (flavor) that might require some tweaking including a mismatch in the size of the armies. I agree with the comments that you can then as a second step scale the smaller army down or the bigger army up in terms of number of elements, depending on what you have in the collection.
Commands & Colors Ancients does this when they size battles for their standard 9x13 hex board and the number of blocks in the game. For the most part it works just fine. Of course if the historical winner rolls 6s and the loser rolls 1s that helps a lot with getting an 'accurate' game.