If you want to make changes without dealing with update hassles:

• Make a child theme to your current theme which inherits from it.
• Add a functions.php to your child theme, which only includes specific overrides for functionality you want to override.
• Presto change-o you are immune to stuff getting ruined with updates. (Aside from API changes and things but those are relatively rare in my experience, for the most part it all just works.)