My mod also makes the Stars and Bars the default flag for CSA on the map (cities and county flag). I have also changed the Guatemalan county flag into the historical flag used during 1858-1871. But I have not changed the floating flag on the GUA cities.
Just drop the folder into the main Civil War 2 folder and accept the overrides. You might want to backup the current files before installing, if you want to revert the changes.
Here is what the CSA changes look like ingame
Also known as wis on the paradox forums.