If you choose to start a new project with React and Webpack, I recommend to use Facebook's official boilerplate[1] and read their really informative user guide. I also find educational to look at the architecture, libraries and configuration of open source non-trivial web applications (e.g. Wordpress Calypso[2]).

[1] https://github.com/facebookincubator/create-react-app

[2] https://github.com/Automattic/wp-calypso