create a .bat file in your gtkradiant directory file.
Edit it, add this line : "q3map2.exe -convert -format map -game jk2 map.bsp" without "".
each time you want to uncompile a map, copy paste this map into gtkradiant directory file, and then edit the .bat, by replacing the "map" by the name of the map you want to uncompile. Once all that is done, you just execute the .bat, and you'll get a .map file, which is the map you wanted.
I warn you : models arn't translated, so you won't have models, textures are all set to default, so you won't have same looking, textures will just be applied to brush, but not edited as ingame, and many triggers/funcs are often bugged.
So basically, what you get in an uncompile is more just the brush of the map, with textures on it and nothing more.