lol it's almost the easiest thing in jk2...
1) find the flag textures in assets0.pk3, they are under /textures/..... folder
2) extract them
3) edit them with GIMP, PhotoShop or even paint xDD
4) create a folder named textures, that contains a folder with he same name as the folder where you found the textures in assets0,pk3, and put your textures in it
5) create a .zip of the textures folder and rename it to putherethename.pk3
6) put the pk3 in ur base folder