OK, so as far as I can tell, the individual units - say “Bajalich” are never present on the board - only their commander - say “Quasdanovich” - are represented on the main map. Is that correct?
However, a commander may also be sub-ordinate to another commander - say “Bellegarde” to “Quasdanovich”. Can the sub-ordinate commander be present on the main map too? That would complicate matters a bit.
How does the Commander pieces on your organisational chart (AutoAOD map) look like? Are they, for example for “Quasdanovich”, a piece that spans several rows and columns - like the gray area indicates?
OK, so that seems straight forward.
That, I don’t quite get. If the large gray piece “Quasdanovich” on “AutoAOD” has the property - say - TotalSP with value 9 - calculated using SumMat - then why would you need to do another calculation to get the same value on the main map? If the commander piece on the map - say “Quasdanovich” is Attached to the equivalent piece on the “AutoAOD”, it can simply get that value with GetAttachProperty. This is by far the most efficient way to do that.
Everytime you use something like SumMap your performance will suffer.
Note that there’s no reason to think that you couldn’t use a pieces name as its attachment name. E.g., the two pieces for the commander “Quasdanovich” - the map representation and the AutoAOD representation - could have the attachment “Quasdanovich”. Yes, you would need to add that trait to individual pieces and they cannot be in a prototype, but on the other hand, it is fairly straight-forward.
Of course, if you use pywargame, you can ensure proper reference in code 
How does the module make that assignment? Is it a user choice, or built in to the module. Again, it may make sense to make this a kind of mutual a
Attachement, depending on how long that assignment may last.
In most of the modules I’ve done, I have logic that allows the user to calculate combat odds. The user selects all belligerents of a combat, and then press a short-cut key, button, or select from the context menu. The module then sums up attacking and defending combat factors - possibly with modifiers due to terrain and features - and calculates the combat odds. An odds marker is then placed on one of the defending stacks and a combat marker placed on all belligerents. The user can then select the odds marker, press a short-cut key, button, or select a context menu item to resolve the combat. A combat result marker then replaces the combat odds marker. If this is something like what you want to do, you can check out one of the modules I’ve done.
How do you set the text labels? Be careful about setting them (directly or indirectly) by a calculation like SumMap - or similar. Every time the label has to be redrawn - which happens relatively often - the expression has to be reevaluated which can potentially be costly. That also applies to Layer trait with Levels follow expression value.
If you use a Dynamic Property - rather than a Calculated Property - to store the calculation in, then a new value will only be calculated on a specific request - for example when a piece is removed from or added to the “AutoAOD” commander piece mat, or when commanders are attached to or detached from a task force on the main map.
Yours,
Christian