Since the card is larger than 32Gb, Windows won't let you format it as FAT32 using on board tools.
1. Option: Format it as FAT32 using third party tools (
http://www.ridgecrop.demon.co.uk/index.htm?guiformat.htm for example). You won't need to fiddle around with updates, plus the FAT32 driver is a lot more stable on the switch. However, FAT32 has a filesize limit of 4GB, so .XCI images larger than 4GB need to be split.
2. Option: Install the exFAT update by whatever method you have access to. This will allow you to use files larger than 4GB, no need to split anything. Just drag and drop. However you should note that the exFAT driver from Nintendo is somewhat unsafe when it comes to write access to the SD card. Therefore homebrew can cause FS curroption on the card when a write process to the Filesystem gets forcefully interrupted. If you're not using homebrew applications (i.e. XCI loading only), you don't need to worry, though.