Upgrade-proof custom settings

Hi all - I'm looking for the best way to add custom settings options to the T3 template manager that is upgrade-proof.

For example, under the 'theme' option you can edit the site name, the logo, the slogan etc. I can hardcode some more options in here, but how upgrade friendly is it?
Is there a better way to do it that straight hardcoding? Any examples of people doing it before?

Thanks!