You can directly modify the theme file, but it’s not recommended. Because the new update of the theme will override your modification. To do customization safely, you should add your customization via the following methods.
Method 1: Child Theme
see Child Themes « WordPress Codex
Method 2: Custom Files
This theme includes 3 files in “detube/custom” directory:
custom.php: for add custom php functions.
custom.css: for add custom css code
Depending on your situation, you should move one of them to “detube” directory, it will working automatically, and the new update will not override it.
Method 3: Theme Options
Go to “Theme Options -> Hook Settings”, there are two fields”
Head Code: for inserting your code before the </head> tag
Footer Code: for inserting your code before the </body> tag
Note:Using this method, you should wrap your css code with </style> tag and wrap your js code with </script> tag.
It’s hard to list which files have been changed, if you really need to directly modify the theme files, you can use some file compare tools to help your find the differences between two versions, so you can merge your modified version to new update easier. (I used TortoiseSVN on Windows and Visions on Mac)