Not sure if there's any documentation (tried the readme?) but it's easy.
Just create a PREFIX_gamefile.txt file in which you keep track of which files should be used by the mod (and use duplicates of the files you change with the same prefix - the same prefix isn't necessary but it's less confusing than giving every file it's own unique prefix ). ModSwapper looks for any *_gamefile.txt files so your prefix can be anything as long as no other mod already used it (which would force users of your mod to manually rename file(s)).
The PREFIX_gamefile.txt file should be of the same format as the regular gamefile.txt files except that you should add 3 things at the bottom of the file: (1) the name of your mod (as it should be displayed in ModSwapper), (2) what file to use for newsprite.txt and (3) what file to use for Great_Library.txt (due to bugs these last two aren't read properly otherwise).
Keep in mind that the language-specific files are all stored in strings.txt, so you effectively have to do the same thing with strings.txt in the english folder as you do for the gamefile.txt in the default folder (and make the new gamefile.txt refer to the proper strings.txt file of course).
Look at the CRA/APOL/MM2_gamefile.txt (and *_strings.txt) files for examples.