How do I update this when downloaded from itch.io? Simply overwrite existing files? Will that retain my progress?

My bad: just copied over the save file directory. Works. :3 

Yeah the download will always have empty save directories and no .config so copiying it over your old game folder should work. You can also get the itch app, which automates the whole update proccess similar to how other platforms handle that.

Thanks so much!