First, some prerequisites - You will need:
- A softmodded 3DS (with SD card)
- A computer
- An internet connection
- The game cartridge itself
Now, if you have a newly softmodded 3DS, I suggest you install the application 'ftpd'. This is not a part of using TWLSaveTool, but is in general a useful application to have on your 3DS for quickly moving files to and from your computer. A guide to installing and using ftpd will be included underneath a spoilertag, then I'll get on with the save backup tutorial.
Now, once in the home menu, confirm that your desired DS game is in the cartridge slot and reading properly. Open the new TWLSaveTool application. Once there, press 'B' to backup the save file. Take note of the filename displayed: for me, it was 'POKEMON SS.0.sav'. You can press left and right to change this, and it will warn you if you are about to overwrite an existing backup.
Once the backup is complete, on your SD card, you should be able to find the SAV file inside the TWLSaveTool folder under the aforementioned filename. You can then take this file and do as you please with it - it's all backed up, so feel free to just start a new game on your cartridge. If you want to restore your old save file, just go back into TWLSaveTool, select the correct file, and press 'A'.
If you want to load your new save file into DeSmuME, all you need to do, is load your ROM file of the game like normal, but before doing anything, go to file -> import backup memory, and choosing the backed up sav file, after you make a copy of it on your computer. The sav file is also easy to load into an application such as pkhex, and a save file modified on your PC can easily be put back onto your cartridge by naming it using the same naming convention as the one you just pulled off your DS, which in my case was 'POKEMON SS.x.sav', where x was the save file number. Just put the modified save file into your TWLSaveTool folder on your SD card, select the corresponding number in the save tool application, and restore!
Have a good day, GAMERS!