Mapping with io-file first method

I've managed to get modding through the io_file first method, and I've made changes in EDU and descr_mount etc with success.

Now I'm hoping to go onto mapping, so I'm wondering if I just directly edit the files that are already there? I did this before in a mod folder when I had to copy all the files, but now I'm not sure what I should do with the io-file first method.

:help:

I use the io.file_first and a mod folder. I keep vanilla as original as possible just in case something goes wrong and my backup doesn't work. Beats reinstalling the game.