I've had an idea for distinguishing brigades unambiguiously :
You need a hole punch, old manilla folder or thin card, blue-tac and highlighters (quantity equal to the number of sub-commanders).
Use the highlighters on the folder or card to create some areas of distinctive colour (or just use different coloured card).
Punch out lots of little discs using the hole-punch in as many colours as you have sub-commanders.
When you are determining your brigades, use a little blue-tac and put a coloured dot on each sub-commander and each unit under his command.
After the game, un-stick the dots again.