@Draxzelex Thanks for that clarification. So form that, I realized that I have only been doing eMMC backups and not emuMMC backups of NAND, etc.
I notice when I flick on "SD emuMMC Raw Partition" that the buttons for backup go grey, and don't allow me to press them. I'm guessing that means that I don't have an emuMMC raw partition, but I do have a separate partition for emuMMC. Given all that, how should I be preserving this? I used a partition manager software on my PC to make a clone of the entire SD card, as in the old emuNAND days of the 3DS, but other than that I'm not sure. Is it as simple as making and restoring an image of the partition, or is there more to it?