Try the following:
1. Copy your Matrix Napoleon in Russia game to another location.
2. Copy the "Main" files into the root NIR folder and overwrite where prompted. N.B. if unzipping, uncheck the option to recreate folders/path.
3. Copy the "Game" and "Map" files into one of the games subfolders and overwrite where prompted. N.B. do not rename the game subfolder into which you are copying the files e.g. to "Ma" for Marengo. If you do this, either the game will not see the folder or the program will ask you for the CD, depending on which version of the game executable you're using. In short, for whichever NIR Project game you're playing, it will have to go into a subfolder called BD, FF, SU etc, or CA, WL, PL etc if it's meant to be used with the BGW game.
Hope this helps. Let me know if you still have problems after this.