Eh, there are several files that might need/could be changed to accomplish this. If you want to change it to a color of a different civ, then that's easy, just go to
Your BtS folder > Assets > XML > Civilizations > CIV4Civilizationinfos (open in notepad)
Find this line for Incas:
<DefaultPlayerColor>PLAYERCOLOR_DARK_YELLOW</DefaultPlayerColor>
And you can just change the color to another already existing color for a civilization by browsing the XML to find the name of the color you want (you probably don't need to do this since all the colors are things like GRAY, DARK_GRAY, LIGHT_GRAY, just make sure that it exists).
If you want to create a new color. That's more complicated, and I have a bad habit of being lazy and just changing the RGB of already existing colors.
That can be done in:
Your BtS folder > Assets > XML > Interface > CIV4colorvals
Make sure your not saving over the existing files, just move them to their corresponding Custom_assets folder, otherwise things might be challenging if you ever want to revert back to default, or made a mistake. This will only change the colors in single player, if you want them to change in multiplayer too you will have to overwrite the original files (keep extra copies of the original just in case, if you decide to do this). Doing this will cause the *MOD* to show up when in multiplayer.
