Create the emuNAND normally, and then move your backed up /Nintendo/ folder into the new location on your SD card (emummc/Nintendo_XXXX, if I remember correctly) so it can be read by your emuNAND. There is no need to delete anything from your sysNAND, since when it comes to your SD contents, you're just moving everything over.
If it's a clean emuNAND (you've never used hacks on it and you intend to play online with it), then you should update in the system settings. If it's a dirty emuNAND (you've used hacks on it), then you should update using ChoiDujourNX, and you should not let your emuNAND connect to the internet (without having
90DNS and/or Incognito installed).