[ILV_Aquila_Noctis]

you can use MAT-Manager for the Markings of the stock nations.
gives you any option of changing RAF roundels to the way you like, as well as any other, also with different weathering options.
You can also make IL2 use your own graphics. I can't do it anymore without this tool.

Doesn't work for non-stock nations though, I have no clue at this point on how to add markings for new nations.

EDIT: actually I also do not know where I must put any new markings for the nation pack, say cratia, within the current mod folder structure. I have a folder with markings but they don't show in the game.
can anyone point me the directories here?

Look at the threads for Gaston's NationsAndSquadrons mod....the problem is, that we den't simply need a folder, but om java too....