Yup. I see that you found the header, content etc. file and the animation is working fine.
From an overview of theme's structure, it looks like different sections are being handeled by different php files.
For instance, the Header and Navigation menu can be customized from header.php, Page titles by page-title.php and so on.
Just one suggestion, please make sure to take a backup of the files before you make the changes
Let me know if you have any other queries.
Please don't forget to rate the Plugin:
https://wordpress.org/plugins/animate-it/