Make a Saturn game and store other files also?

Sounds to me that rvddx is trying to take a Saturn game (ISO or CD), extract all it's files to HDD, add a folder of other files into the same directory where all the game files are extracted to, then re-master that back to a Saturn ISO and patch the boot sector back in.

In terms of re-mastering a game ISO, it's possible as evident with Alex Kid's Ninpen Manmaru Project. So I guess it's possible to add in a folder of extra files (e.g., FAQs, CD covers, etc.) as well. Give it a try. One problem I think you may run into is if the game contains multiple audio tracks.