Hi The Emperor. Well bascially you've got :

SetShieldImage:: FN_BURGUNDIAN "Burgundy_lge" "Burgundy_sml" "Burgundy" "F1014" "F1014"
FN_BURGUNDIAN
this declares the faction in which u shall find the flag shields that represent the faction.

"Burgundy_lge" "Burgundy_sml" "Burgundy" "F1014" "F1014"
these are the faction shields that will appear in the game. This are found in the following folder "Total War/Medieval-Total War/Battle/Flags.

These can be easily modified using a BIF Reader. If u don't have one, here's the link to it: please click here

Hope this helps!

Thanks,
Aenarion