Saw this earlier...
To separate emunand from sysnand, boot into sysnand, go to settings and on the last page (with the format option). Once you're there, remove the SD Card from the 3DS then format the 3DS (it'll require an internet connection but won't update, don't worry). Once it's formatted, the 3DS will reboot. Once it's rebooted and the 3DS is on again, put the SD Card back in the 3DS, then do the first setup again. Once the setup is done, it'll create a new folder (different from emunand).
After that, it's done, your sysnand and emunand are separated and configuration on one (theme, settings, programs) won't affect the other one, and you won't have to unwrap your gift each time you boot.
Look right?