Not an emacs user, but probably there's an option for emacs that will allow you to embed your emacs config into your nix config.
If you'd rather have a separate file, you can install files to /etc/ via the environment.etc."<file-name>".source = ./file/in/your/nix/repo
or using home-manager with home."<file-name>".source = ./file/in/your/nix/repo
I'm a "put it in the nix config" guy myself, and that's how I set up neovim