I assume by "added on cfw" you mean "added on emuMMC". If you want a game to be available on emuMMC only and not on sysNAND then there is no need to use the same nintendo folder for both sysNAND and emuMMC, and in fact I would recommend not to. So all you have to do is install the game after having booted emuMMC (with goldleaf for exemple). If you chose to install it to the internal storage everything will be in the emuMMC partition, if you chose to install it to the SD card then most of the game data will be in the Nintendo folder associated to your emuMMC (so by default /emuMMC/RAW1/Nintendo). The only reason to merge both Nintendo folder is if you have some games installed on your sysNAND, create an emuMMC partition from this sysNAND and want to be able to lauch these games on emuMMC without duplicating your Nintendo folder (which obviously takes double the space). Since you're talking about installing a new game there should be no need for you to copy the nintendo folder nor to edit your emummc.ini.