I’d recommend using PackageResourceViewer to open the file.
You could make your modifications there, and it would save in the proper location to override the built in files.
However, I would recommend copying the contents of the file and creating a custom version in your User folder. That way, you can easily move it around and modify it without worrying about the built in color schemes.
In ST3 the path is Sublime Text/Contents/MacOS/Packages/Color Scheme – Default.sublime-package but using PackageResourceViewer you don’t need to know that , you can just:
Command Palette -> PackageResourceViewer: Open Resource -> Color Scheme - Default -> [the theme you want to get at]