By meta boxes I assume you’re referring to different ACF field groups or fields..
This is basically all about the themes coding, you code the fields where you want them and thats it.. If you want the user to be able to switch position of the fields outputted content simply from the admin you could try take a look at the Flexible field addon!
Welcome to the Advanced Custom Fields community forum.
Browse through ideas, snippets of code, questions and answers between fellow ACF users