@hr_oskar
1. when i test a game, then i look also how the symbol looks with the colors, if it's better that it uses the first or the second color. since i use in my mod some flags where the symbol uses the second color.
also, i know that it's difficult to choose the color-use (black symbol, white bacground - white symol, black background) for a official flagpack. but it should be easy to invert the flags yourself also. (explaination follows)
2. i don't know how it work with gimp, but i heard that it can handle .dds-files. i use DXTBmp for the .dds. with this tool i can export the normal pic and the alphachannel. as inport-programme i used MSPaint and now i use a prgramme, that i bought some years ago and underestimated it. it is Micrografix PicturePublisher. if you get DXTBmp, then you could easily export the alphachannel pic of the desired .dds into mspaint (for example), invert it, re-inport it into DXTBmp, save and you have it. for that, i don't know how gimp works. i read a little bit in the thread about it.
3. when i go to flagmaking, then i do it so:
-at first, i search a big enough picture. then i try, that the desired picture will look good in black-white, use some "masks" (or "templates", don't know the proper word) to define the border of the symbol to the background, that it will look good when i convert it to a black-white-picture.
-then i cut out the symbol and add symmetrically the picture around it. now the symbol should lie exactly in the middle of the pic. when that works, i convert them back to RGB and then i save it as my mono_XX.bmp.
-now i can do the main flagdecal. at first, i convert it to greyscale. then i stretch it in width about 30% (ex: 200x200 -> 260x200). that should compensate the ingame stretch-effect.
-to get a squared picture again, i add the picture in heigh at the top and the bottom. since the symbol on the ingame flag is naturally to high if it's in the middle, i add the picture on top 2/3 and on the bottom 1/3 of the picture (ex: 260x200 to 260x260 --> add alltogether 60, devided into 40 on top, 20 at bottom). now the symbol is out of the middle in bottom-direction.
-now i resize the pic to 128x128, with the "smooth size" option activate (hope you know, what i mean). then i mostly have my flag-image. just some adjustements after testing ingame, then exporting it to the DXTBmp and save as DXT 3 DDS.
4. i'm not sure i know what you mean with "layers". as said, i don't know how gmip works, but i don't use layers.
i hope you understand how i do it. it is hadly to explain in a foreign language even when i don't know how i would explain it in my mothertongue
