With FBI you can:

• Browse and modify files
• Export, import, and erase save data from DS cartridges
• Install titles/tickets from a file system, over a local network, or over the Internet with a URL or QR code
• Browse and delete pending titles (downloaded updates, in-progress eShop titles, etc)
• Customize appearance by placing replacements for RomFS resources in "sdmc:/fbi/theme/"

And more! You can find instructions for downloading FBI here, however if you've modded your DS using the 3ds hacks guide, it should already be on your console.

Universal Updater can:

• Browse homebrew applications and view information such as version number, release notes, screenshots etc.
• Automatically download, extract, rename, and place files for simple one click installation of apps
• Sort and search for homebrew, or add markers to easily find your favorite homebrew apps
• Change UniStores to view different repositories such as TWiLight Menu++ skins or create your own

It is quite simply a manager for everything homebrew on your console, including helpful tools and community made ports of non-DS games. You can find instructions for downloading Universal Updater here, however if you've modded your DS using the 3ds hacks guide, it should already be on your console.

You can use checkpoint to:

• Export and import saves, both 3DS and DS titles
• Creation of cheat files for various games
• Modify Play Coin count

Checkpoint is basically just a cheats app where you can mod your games, get cheats, give yourself things etc. as well as manage your actual save files. You can find instructions for downloading Checkpoint here, however if you've modded your DS using the 3ds hacks guide, it should already be on your console.

FTP is just a software you can download to your console to be able to access your files wirelessly from a computer on the same network. It's as helpful as it sounds.

You can find instructions for downloading and using FTP on this helpful website I found.

If you've done any research into running GBA games on a DS, you will have heard the name GBArunner2 thrown about. You do not need to use GBArunner2 if you're using the Twilight Menu ++ custom firmware (which you will do if you modded your Old or New 2DS/3DS using the 3DS hacks guide website). You can use the 'EVERY OTHER ROM' section of this page to learn how to better run GBA games on Twilight Menu ++. The reason you shouldn't use GBArunner2 on Twilight Menu++ is because not every game runs well on it, but if you insist on using it or have a DSi console, then here is the wiki for the software plus an extensive list of compatible games. I believe you can download GBArunner2 from Universal Updater.