I decided to go with the Generic Major and Brigadeer leaders for stuff that did not have an actual leader portrait. See the attached pic. They look nice. You can arrange the nomainclature that displays on the Detail Popup to describe these officers as Staff.
And for converting the Great Lakes to ACW, I went with a Regimental game, like the BoA original. I used all the original unit names and general names. They are all dressed up for ACW now, so they need the generic leader graphics. I ditched the Indians and substitued "Native Militia" units instead.
The notion of eschelons is not part of the BoA database, and the system can support anything you like (Regiments, Brigades, Warbands, Legions). And each type of scenario can be integrated into the same game.