I can make neither head-nor-tail of your folders/files. Your Graphics folder appears to contain multiple folders for separate leagues with your faces cut-outs sitting alongside them. They need sorting out. I can only recommend that you match what I have...
Within your Graphics folder, sort them into separate folders for:
- Clubs — Team logos sorted into separate folders by country
- Competitions — All competition logos in one folder
- Continents — Logos for UEFA, CONCACAF, AFC, etc.
- Faces — Any facepacks that you use, with everyone in the same folder
- Flags — National flags, sorted into separate folders by continent
- icon faces (if you use them) — Should just match the content of your Faces folder
- Kits — You should have the SS Kits Default that comes with the game, SS Kits Updated containing any kits graphics that you have downloaded, sorted by nation and division (e.g. England_Premier League, Germany_Bundesliga, etc.) and any 3D Kits that you may have downloaded
- Nations (National FA logos) — These are all in the same folder
- Stadiums (if you use them) — I have these on-file but I don't like them in-game so I don't use them
- Trophies (if you use them) — All in the same folder.
Then once you've done that, your issue regarding National FA logos and Flags showing where you want them to can be resolved by making sure that your config files are giving the correct instructions, as per this screenshot (flags on the left; national FA logos on the right). If you do all that, it should make your graphics behave the same way as mine, which (I'm pretty sure) is what you want...
