Override CSS the best way with Yootheme templates #1528
You can create a new style in the Customizer. This creates a new folder in the /styles/ folder. Here you can add a custom.css in the css folder. This way you can update your template with out your changes going away.
You can also add a folder called /layouts/ and adda copy of the theme.php and make changes here. That way you can create new positions for modules and change all details of the template.