There are many settings for this plugin so please refer to the plugin documentation for an explanation of all of them. There is one however that I would like to mention.
Enable WooCommerce CSS
This option is found in the "General" tab in the settings page of the WooCommerce PLugin. WooCommerce>Settings>General(tab).
Scroll down to a sub section called "Styles and Scripts" and check the box beside "Enable WooCommerce CSS". This will reveal several color pickers which you can use to assign a custom color to some of the elements in the plugin which are not controlled by the theme's primary color choice. The "Proceed To Checkout" button is one such element.
This setting will probably be enabled by default in most installations.