Ok everyone I finally figured this one out. Here's how you do it.

Player::"Takeda Shingen_xzy" 5 5 LOCAL "Takeda Shingen" 0 true
17383 8289 180

In the "battle".bdf (with "battle" being the name of the battle in question) file, the first of the 2 #'s after The "General's Name_xzy" determines the unit flag colors for the Specific General. Here's The key:

0 = White (Rebels & Ronin)
1 = Green (Shimazu)
3 = Yellow (Oda)
4 = Light Blue (Imagawa)
5 = Black (Takeda)
6 = Purple (Hojo)
7 = Blue (Uesugi)