I prefer to maintain a single file, webpack.config.js. This allows me to extract commonalities between different build targets to a common structure of its own. I manage composition through webpack-merge (disclaimer: I wrote it).
In the setup of my free book I pushed the level of abstraction so that I maintain higher level configuration at webpack.config.js and then compose it using webpack.parts.js functions. This becomes particularly useful as your configuration grows.
The repository contains other configuration files designed for particular demonstrations and you would most likely skip most of those in practice.
There's no single right way to manage webpack configuration. You have to find a way that suits your way of working. I prefer a composition based approach myself, but your mileage might vary.