It's been awhile since I did it, but I think I was using these tutorials at the time, and I just dumped everything, even if it was claimed to not be used by Citra.
https://citra-emu.org/wiki/dumping-save-data-from-a-3ds-console
https://citra-emu.org/wiki/dumping-extra-data-from-a-3ds-console
https://citra-emu.org/wiki/dumping-system-archives-and-the-shared-fonts-from-a-3ds-console
https://citra-emu.org/wiki/dumping-config-savegame-from-a-3ds-console
I then used a website that told me how the folder structure on the 3DS was laid out, and tried my best to match that to the folder structure for Citra's User folder. I don't remember which website it was, but the layout for some of the dumped folders don't match exactly, so you have to work out where Citra expects the files to be.
It's not as hard as it sounds, however since I don't remember exactly what I did, I can't really be much more help with this. Still, I hope this helps lead you in the right direction.
Edit: As I said, make sure you dump everything, and put it in all the correct folders for Citra, and it should work. You will also need a dump of your save and extra data for each of the system apps and games that use Miis if you want your Mii characters to show up correctly.