Boot into HomebrewLauncher and use svdt. Then find the Game you want to load data to. When you open it, it will ask you to either enable secure value rewriting(A button) or disable it(B button). Press the A button. You need this, because .CIA games and every eshop game have some digital keys or something like that(something something digital keys). xD I'm not really sure myself. After you have enabled it, load the save file and voila.
I tried it on my Pokemon Y on EMUNAND(NOT sysNAND) using svdt to backup the save file, but I never edited the save it and never loaded the new one. On ProjectPokemon they told me it will work. But, just to be sure, wait for another input from someone else as well.
Edit: You can also use savedatafiler since you can install .CIAs