There are a few things that you can do.
What I've done for the Berlin scenario I'm working on, which has US, UK, French, West Berlin Police on one side and East Germans and Soviets on the other, is I merged the data files together using some excel concatenation functions where I added a letter code to each nation's weaptag number in the weapon lists (an American M16 changes from "SA5" to "USSA5"), then update the weapon list in the units tab using more concatenation functions to reflect the changes. That way each nation's units are using their correct weapons.
In the PICID, I've added a nation letter tag to the bitmap name. I've then used batch processing to add each nation's flag to the all unit bmps in the common data folder and save them in the BerlinAllies nation folder. This will allow each allied nation to have unique unit pics, check the infantry units below for an example. It does quadruple the amount of pics the game loads but as they are only 8mb total per nation, it's not a big issue. I've also given the allies a common counter background, in this case blue.
