Tools like Kami_Sama's Theme Editor or Usagi 3DS Theme Editor allow you to package your images and audio into a .zip or .cia file.
If you are diving into the 3DS Theme Archive specifically to collect rare treasures, look for these:
Visit the official (search on Archive.org or major GBAtemp forum threads). Look for the "Complete Collection" torrent or individual region packs.
host approximately 40GB of data, encompassing thousands of official releases. Custom Themes