First you need to figure out what you need to change to make whatever changes you may want (this may be a fixed position in a fixed file, a fixed position in an arbitrary file if it has multiple save slots, a file inside a standard disk image, a complicated proprietary filesystem in games like Pokemon gen 3...)
Then write code to perform that change
Then, most games have checksums and/or signatures (again in completely arbitrary locations): locate them (a decent way, for games not loaded with analytics, is to compare 2 saves made one after the other without doing "anything" in-game), figure out what type of checksums they are, and write code to recalculate them
Note how all of the above is not specific to 3DS (assuming you're working with decrypted saves = SaveDataFiler, svdt, JKSM...) nor to "PC" (for which operating system would matter too)
You may want to make some convenient, possibly graphical, user interface: that and some implementation details, are where the platform you're writing for ("PC") will matter, but the bulk of the thinking is not there