Same way you do on any other OS with a file explorer--install them to sd:\apps just like any other app.
To install games to your USB loader, your USB drive must be formatted into FAT32 if you want to install GameCube games. Use the app CleanRip (or your USB loader's "install" function, although CleanRip is generally better suited for this) to rip discs to your USB loader.
...am I missing something? What exactly is it that you're having a problem with doing?