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.
1. Install and launch TWL Save Tool from GitHub. Mirrors of v1.2 can be found here (CIA version) or here (homebrew version).
2. Click "B" and wait for