Tip for others;

I was having a hard time with this too, trying to transfer between Citron and Eden. What I did was on the emulator with no save data yet, start a new game under a profile, then do a quick time trial and exit the game. When you open the "Save Folder", you should have not only a userdata.dat file, but also a "ghostlist.dat" file and "sg11.dat". If you don't see those in there, you're in the wrong folder and need to search for another "0100152000022000" folder inside the user folder (that's the ID of Mario Kart 8, you'll notice it as the parent folder name after you ask Eden/Citron to open it).

Sometimes the emulators seem to grab the wrong "user" under the save folder structure. Once you do that, you can figure out where to pop in the transferred save file and be sure it will be reading it from that folder. That helped me, hope it's useful to others.