Sometimes theme authors ask you to add code in functions.php and you can use that.
There is another option. You can use a so called Must-Use plugin which doesn't have to be activated.
WordPress runs it automatically. It will show up under Plugins > Must Use
I have created a sample plugin that you can use to add extra functionality.
https://raw.github.com/orbisius/orbisius-site-util/master/orbisius_site_util.php
How to install it?
1. Create a folder called wp-content/mu-plugins/ (if it doesn't exist yet)
2. Save/upload the file in as wp-content/mu-plugins/
3. Add some functions in the function called 'orbisius_site_util_after_setup_theme'
4. Done.
Troubleshooting
Note: if you make a php error ... your site will crash. Don't panic. Try to see if there is a closing bracket or a semi-colon missing.