JKSM is an older 3DS save manager, but can still be safely used if you are using homebrew instead of CFW, or if you'd rather not use Checkpoint
JKSM's GitHub page has been removed, so look here for downloads:
JKSM.cia (for CFW)
JKSM.zip (for homebrew)
CFW is the preferred way to use JKSM. If you are using homebrew instead, skip to "Using Homebrew" below.
1. After installing JKSM with your favorite CIA installer, open JKSM on your 3DS and click on either Cartridge or SD/CIA, depending on whether you want to backup or restore a cartridge or installed title.
2. Scroll down to and click on your desired game. You may need to click "Refresh Games" on the previous Screen if you don't see your desired title listed.
3. Click on "Save Data Options" then click on "Export Save". Click on "Import Save" instead if you are trying to restore your edited save file back to your VC Game.
4. Click "New" and create a new folder to put your save file in.
5. Exit JKSM, Power off your 3DS and put your SD card from your 3DS into your computer (if you use an FTP client on 3DS you can alternatively launch it instead). Then navigate to (JKSV/Saves/"your desired game"/"your folder name") Inside should be your save file.
6. MAKE A BACKUP OF THIS FILE BEFORE USING OR EDITING IT WITH ANY SAVE EDITORS.
The steps for using homebrew are a little different than for CFW:
Download JKSM.zip and copy the 3ds folder to the root of your 3DS's SD Card.
Open the homebrew menu using your favorite homebrew entrypoint.
Choose JK's Save Manager, and target the game you wish to manage.
Resume from step 3 of "Using CFW" above.