I'm not too clear on mounting the internal sysnand or the emunand file/partition.. the emummc Nintendo folder, and the regular sysnand's one are easily accessible, though. it's the same as on 3DS, just find the game by title ID, and copy the save data over to wherever you need. it's usually "main" or some nondescript file.. better to just drag the whole folder, probably. you'll have to reinstall the game because of tickets or something, but yeah.
edit: I think you can mount sysnand on pc thru hekate or some kind of tool. I don't know if it has its own Nintendo folder for when you don't install to SD or what. If all saves are naturally on the SD's Nintendo folder, then everything's good. Back to looking up the title ID and just copying the folder over the one made when you reinstall the game on emunand. It's a lil annoying but the save data is usually most important anyways, I'd assume