Well, backing up the data on the SD card is trivial, with either tar or dd. Then to restore, you'd just mke2fs+untar, or dd the whole mess back.

If you want a magic solution, Acronis True something-or-other is said to work well. Never used it.

(I think there's some stuff from the 0xffff project related to building a Fiasco image from a booted (and configured) device, but the easy thing to do is leave the main flash basically stock with some recovery-type utilities, clone to SD, and do all your configuration there. Then, if you want a backup to restore the SD, like I said above. Worst case, if you somehow burn both the flash install (that you don't generally use) and the SD, reflash to a stock image, install the bootmenu, dump your backup onto old/new SD, and you're good to go.)