Homebrew apps can be unreliable, but JKSM tends to work without any problems for me. Are you using the version from ...? Do you have jksm.xml in the same folder as jksm.3dsx?
I don't think Checkpoint works from the homebrew menu at all. Also note that the 3dsx version of JKSM is quite incapable of backing up Mii Plaza saves.
I found a *super* generic save manager on reddit /r/3dshacks/comments/3j273o/save_manager/ that seems to export saves, but I do not trust it. It throws everything in the same folder and crashes often. I tried JKSM from github. But that didn't work out, so I'll give that version a try. Thanks! I'm not worried about Mii Plaza.
Using fuse-3ds, you can do all the decrypting and extracting with a Windows PC, if you're so inclined.
You can also use fuse-3ds to extract data from a NAND backup made using godmode9, including Mii Plaza save data. (But, again, you won't be able to re-import it using JKSM.)
And fuse-3ds only needs movable.sed? I was a little confused when looking over it yesterday, since it mentioned seedDB. I don't want to put CFW or anything more than homebrew menu on my main N3DS. I have a lot of money put into my eShop account there (which is shared with my Wii U & Switch), so I'm not willing to risk anything.