I got into that kind of stuff only recently, so I’m far from an expert but the way I see it you got 2 ways of doing it:
a) have 2 entrypoints in your webpack.config.js, one for client one for server
b) only have an entry point for the client but have an extra js file that requires the server js and uses babel-register to transpile that:
presets: ['es2015', 'react'],
plugins: ['transform-decorators-legacy', 'transform-class-properties'],
In my current setup I got hot-reload working for the client stuff and use babel-register for server. When I had 2 entry points it made it so, that hot-reloading wouldn’t really work (and I got that yellow warning that modules don’t know how to reload themselves - so you’d have to manually reload the page). Note that babel-register shouldn’t be used for production though - you’d just serve the pre-transpiled file in production.
Hope that gives you an idea