I don't know if this was a problem for anyone else but it was VERY confusing for me so I will make a simple Guide.
How to use 64 GB + SDXC Cards with 3ds
- Download MiniTool Partition Wizard, install it
- Plug in your SDXC into the computer
- Choose your card (BE VERY CAREFUL YOU PICK THE RIGHT ONE!) and delete its partition
- Create a new partition in the unallocated space "Create As: Primary", "File Sytem: FAT32", and "Cluster Size: 32kb" (Make sure your drive has a letter name)
- Hit ok, then apply in the top...
How to use 64 GB + SDXC Cards with 3ds