I use Checkpoint to manage saves.
Once installed on your 3ds, opening it will populate the menu with all the installed games you've opened at least once, and you can use the dpad to select a game and press A. There's a menu on the touch screen. You can backup or import saves, and choose a name for your backed up saves. There's also cheats
, and a Switch version.
Make sure you've opened the game you want to edit at least once. Open this app. It'll take a while to load for the first time. It'll create a folder named "Checkpoint" in the "3ds" folder on the root of your SD card. Inside you'll find "saves". On your PC, find the right folder inside here with the game's name, and drop in the folder with your save.
Example: sdcard/3ds/Checkpoint/saves/0x0055D Pokémon X
The folder's name contains the game's title ID (the part that's different from other games, meaning without all the zeros), and the game's name. Drop your save in this folder.
Back in your 3DS, open checkpoint. Select your game. First, 'backup' your current save in case you mess up or change your mind, feel free to rename. Then, 'restore' the save you want to import. You select a game with A, choose a save with dpad and backup or restore with L/R. Press B to cancel and choose other games. Press Start to safely exit the app.