You need to separate the sysnand from emunand. Initially, they use the same folder on the SD card (that's why when you setup a theme to emunand, sysnand get the same theme too, and the contrary is also true), so yes, he answered the question.
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.
With this trick, you can also delete cia programs through the data management menu. When sysnand and emunand share the same folder, going into this menu remove everything but once sysnand and emunand are separated, you can access it without any risk.
You can get eshop stuffs with the nnid but there is always a risk of losing them, of course. My brother got all the things he bought back on emunand without any problems (dunno if it would have worked on sysnand), but the other 3DS I tested didn't managed to get all the stuff back on sysnand.
