I'm really bad at this. I have like 30 different NAND backups all over the place with really crappy labels/foldernames. Makes matters worse when you're trying to keep O3DS/N3DS separate. For A9LH stuff I just made a folder "NAND BACKUPS 9.2/10.7 BEFORE/AFTER AL9H", have the files appended with original/a9lh respectively, and a readme describing the state of each and which to restore if things go screwy. It's too important to get confused. I also have the OTP in there.
Hey, I have a good suggestion. I have backup files for five different consoles, I named each folder with console serial number, that way you will by no means to get confused. Maybe you can captions such as "XXX's N3DSXL Red" next to the serial numbers.