If you are trying to back up your cartridge save for Gen 4-5 using TWL Save Tool, there are a few things you will need. The main device I will be using in this tutorial is a hacked 3DS. You must either have CFW or Homebrew. If you use the Homebrew version, you must have either PokéTransporter or Pokémon Dream Radar installed on your 3DS.
2. Click "B" and wait for the save to be read from the cartridge (Note: if you wish to restore your save after editing in PKHeX, click "A" instead of "B". This will overwrite the save on the cartridge so MAKE SURE YOU HAVE A BACKUP)
3. Turn off your 3DS, eject your SD card and insert it into your computer. If you use an FTP client for the 3DS, you can alternatively launch that instead.
4. Navigate to the "TWLSaveTool" Folder where your newly created save should be.
5. MAKE A BACKUP OF THIS FILE BEFORE USING OR EDITING IT WITH ANY SAVE EDITORS.