You copy /includes/languages/english.php into /includes/languages/your_template/english.php, or /includes/languages/english/contact_us.php to /includes/languages/english/your_template/contact_us.php, and make your changes there.
When you upgrade, the new /includes/languages/english.php stays as is.
Keep a record of all files you have made override copies of.
Look at the changelog for the upgrade and see if any of your overridden files are mentioned; if they are you need to compare the new with the original to see what was changed (make notes including line numbers), and then compare your copy with the new and replace the changed lines into your copy.
If a changed line was also customized by you, you will have to reconcile them. You are unlikely to run into that until you have made fairly advanced mods. You need to do some work, but your override copies will never be automatically erased or replaced. I have found that two or three out of a dozen overridden files typically needed to be compared.