There's this homebrew software called Checkpoint (google "Checkpoint switch" and you'll get it) that gives you access to your save data. If you boot into sysmmc and launch checkpoint, you can get your save data. Then, you can boot into emmummc and install your save data there.
Tbh, I don't see much of a point in using the above approach when you could just use a new system account. If you make a new account on your switch, that will work as a way to get a new game on totk. I guess the only benefit of going the checkpoint route is if you want to also play with your save in an emulator.