This is the standard tool for installing CIA files; ensure you have the latest version.
To help me tailor more information for your handheld setup, tell me: Are you using an or a "New" 3DS/2DS model?
Full retail games, Virtual Console titles, and digital-only releases (eShop exclusives) installed directly to your home menu.
The 3DS officially supports up to 32GB cards, but can easily use 64GB, 128GB, or even 256GB MicroSD cards if formatted to FAT32 with a 32kb or 64kb cluster size. Larger cards allow you to keep dozens of large retail games installed simultaneously.