To change the character portraits extract the basicMod.zip file that is provided with the game and you can find in the ./mods folder. Extract the basicMod.zip into the mods folder. Then open it and navigate to the ./mods/basicMod/gfx/ui/portraits. There you can find all the portraits that are used ingame.
If you want to change one just overwrite an existing one and the game then integrates your new one into the atlas.