I actually bothered to read the FW article (being a ToT-er) and I guess it ain't the best, particularly the section on civ colours. I've attached an image to make it a bit clearer. Note the exact position of the pixels:
1. Determines the font colour for the city name.
2. Determines the colour of the unit shield, and city size and revolt boxes.
3. Determines the colour of the back shield when the units are stacked.
The screenshot shows all three in combination, based on the flag to the left.
Does this help?