So in your first file that it pregenerates is an array. In that array you create an initialization for the cfg file you want. So lets say in the array you put "myTweaks.cfg" exactly. Then in that folder you create a file called myTweaks.cfg (make sure you convert the file to cfg and not just name it that.) Then copy your code into myTweaks.cfg file:
myBiomes = forBiomes(4, 1, 16, 2, 5, 0)
myBiomes.removeAllSpawns("CREATURE")
myBiomes.removeAllSpawns("WATER_CREATURE")
myBiomes = forBiomes(4, 1, 16, 2, 5, 0)
myBiomes.removeAllSpawns("CREATURE")
myBiomes.removeAllSpawns("WATER_CREATURE")