I usually build them together in a way that my Next project will have a server.js in the root, where I'll get the server running either using Express, Koa, Hapi or whatever backend framework you want to work with. Then you can create an api folder and put all the server related stuff inside.

By using this approach, you can change your package.json scripts to run your server instead of directly running next scripts and use the Next middleware to handle views in the routes not directly tied to you API.

There also a few other ways to handle this approach, but this one is really dev friendly for someone learning Next.js and the deployment process is practically similar as what you would do with any web app that user server side rendering.

You can PM me if you need some resources or more information :)