There are multiple ways to transfer 3DS save data to Citra in a usable form, but the important thing to note is that whatever tool used to get the save data off of the 3DS supports exporting expanded save data.
Save data lives in Citra’s emulated SD card directories (user/sdmc/Nintendo 3DS/000...0/000...0/title/[game-TID-high]/[game-TID-low]/data/00000001/).
threeSD is a tool written to help import data from your 3DS for Citra more conveniently.
Refer to threeSD Quickstart Guide for importing your installed titles, updates, DLCs, save data, extra data, system files, etc. Note that you’ll still need a hacked 3DS with GodMode9 to obtain your keys so that threeSD can decrypt the data on your SD card.
As the supported way of transferring save data, Checkpoint is easy to install and use.
/3ds/ on the SD card. Hax-based Homebrew Launchers are not supported by Checkpoint.Backup on the bottom screen. You will be prompted Yes or No. Select Yes by pressing A.OK on the bottom screen.Success! Progress correctly saved to disk. Exit out of Checkpoint./3ds/Checkpoint/saves/[Game Name]/[Folder created in Step 4] to the computer.
"User directory"
└── sdmc
└── Nintendo 3DS
└── 00000000000000000000000000000000
└── 00000000000000000000000000000000
└── title
└── 00040000
└── 0007ae00
└── data
└── 00000001
└── BigRedSave.dat
In addition to save data, some games and system applications use extra data. Game extra data is stored on the SD card and can be extracted and used by Citra.
Backup on the bottom screen. You will be prompted Yes or No. Select Yes by pressing A.OK on the bottom screen.Success! Progress correctly saved to disk. Exit out of Checkpoint./3ds/Checkpoint/extdata/[Game Name]/[Folder created in Step 4] to the computer.user folder. These directories may have to be created if the title the extra data was dumped from hasn’t been played in Citra yet**.
"User Directory"
└── sdmc
└── Nintendo 3DS
└── 00000000000000000000000000000000
└── 00000000000000000000000000000000
└── extdata
└── 00000000
└── 000012C8
└── user