Have you followed the GDNative tutorial on the Godot documentation? If not, I would suggest trying to mirror it exactly at first, and then make small changes until you get a file structure you like.
Other than that, I’m not really sure. To the best of my knowledge, there are not too many C++/GDNative developers here on the forums. I would suggest making a post on Godot’s Facebook, Reddit, QA, and/or Discord and see if someone there knows more about GDNative and can help.
