It seems that
@Sykoh is reading the older guide. There's a new one using Decrypt9 to inject a CTRNAND already in 2.1.0.
@Sykoh, try reading the new guide from here:
https://github.com/Plailect/Guide/wiki/Homebrew-Launcher-(Browser)
Since you already use *hax and CFW you can try using Decrypt9 directly from homebrew launcher.
Using Decrypt9 you will want to do a backup of your emunand partition and restore it at the end of the guide instead of restoring your sysnand backup (but I strongly recommend that you do both backups in the case that you ever want to restore a clean sysNAND back).
You won't need to format your SD card if you want to continue using emuNAND for whatever purpose, but if you want to format it to reclaim the space used by emunand partition (using SDFormatter with size adjustment on or emunand9 format options) you have to backup your Nintendo 3DS folder and copy it back after formatting.