Create a special source folder for your project.

Never change original source files — edit the copies in your custom source folder.

Tell the Potato where to look for source files (Control + Alt + Shift + S).

Pick a "handle" and use it to identify all your modifications (e.g. "MDH_Custom")

Comment out original code, but leave it there rather than deleting it.

Explain your changes in comments.

Maintain standards-compliance (& validate!).