I originally tried JosJuice's suggestion of HW.cpp, but either it caused a desync problem that wasn't there before, or I had some settings wrong. I ended up messing with nandpaths.cpp instead, and while it does work for saves online, you can't use the Wii remote offline. No doubt there are better ways to do this, but I wouldn't know how. I would also suggest starting from a new folder with portable.txt because there are some things that can cause a desync here that didn't seem to be a problem on 6502. Despite that suggestion, it should still be safe to import a save file before starting a game or to use your Mii file.
https://github.com/SuperDavid2/dolphin/blob/master/Source/Core/Common/NandPaths.cpp Here is the actual file I changed along with a link to the repository itself. https://github.com/SuperDavid2/dolphin
I will wait to see if it's ok to share Dolphin.exe. If I messed up the whole github thing, I will fix it when I find out what the problem is.
https://github.com/SuperDavid2/dolphin/blob/master/Source/Core/Common/NandPaths.cpp Here is the actual file I changed along with a link to the repository itself. https://github.com/SuperDavid2/dolphin
I will wait to see if it's ok to share Dolphin.exe. If I messed up the whole github thing, I will fix it when I find out what the problem is.