How to center entire website?

You should never make changes directly in any of the WP Twenty XX themes. Always use a Child theme or your changes will be lost if you update the theme.

For CSS changes you can use a CSS plugin such as Simple Custom CSS to make your changes.

You can test this by adding it to the end of your theme’s style.css, but to make it permanent, you should do as suggested above:

.site {
   float: none !important;
   margin: 15px auto;
}