The folders in the mods package will only have the files edited by the mod team and thats all, so if you copy for example the Program\scripts folder over to the game directory you will infact only have 1 out of about 23 files so your game wouldn't work. So if you have copied folders over then get ready to reinstall COAS because when you hit launch the game will not load and even if it did it would crash soon after
Luke i'm sorry to contradict you but when you paste a folder which have the same name of an existing one, windows warn you that you will overwrite files with SAME names. It doesn't erase content of the original folder.