Here are all the things you can do:
- Taking out SD card (normal way)
- Setting up an FTP connection (basically lets you send files over your wifi to your 3DS)
- Uploading them somewhere and downloading them with the MultiDownload++ homebrew (most roundabout method)
I suggest just using FTP if you mind taking out the SD card that much, may seem a bit complicated at first but if you read up on it and manage to set it up, you will see it's simpler than it looks.