Secondly, the dotfiles. I hear there is the Home Manager for that, but it doesn’t have support for everything

In this case, you can use home.file option of home-manager similar to environment.etc of NixOS configuration.

For example, let's configure dunst with home-manager [^1]: [^1]: https://nix-community.github.io/home-manager/options.xhtml

# installing the package
home.packages = [ pkgs.dunst ];

# configure dunst

## writing new config
home.file.".config/dunst/dunstrc" = {
    text = ''
        [urgency_critical]
            timeout = 15
    '';
};

## using existing config
home.file.".config/dunst/dunstrc".source = "/path/to/existing/dunst/config";

services.dunst = {
    enable = true;
    # using existing config
    configFile = "/path/to/existing/dunst/config";

    # new config
    settings = {
        urgency_critical = {
            timeout = 15;
        };
    };
};

Is there a way to manage everything at the same time?

Yes, create a git repo and keep your configuration there. Don't keep secrets unencrypted in there as those will end up in world readable /nix/store. Any user where system or human can access those. You can use any scheme to manage secrets at wiki^2.

Even better if everything is in configuration.nix

You can do everything in single file but I wouldn't recommend it as configuration may grow quickly and be difficult to manage later. Instead you may split the configuration.nix into multiple files and import those in configuration.nix.

Flakes simply helps to manage the inputs easily (e.g. nixpkgs, home-manager), i.e., which version of input your config uses. Traditionally inputs is managed by nix-channel imperatively. It generates flake.lock to store the hash of inputs which won't be updated unless you update it. If you copy the config between different machines (or reinstall), you'll get exact same version of packages. It also helps avoid adding nix-channel, which you have to add manually during reinstall and you may not get the same version of packages. So, it's not important as you can do all things with/without it.

I found this guide ^3 quite helpful to start with flakes. You may use one of Misterio77's starter configs^4. Also, a big surprise with flakes is that if you don't use git, then your all files from config dir will end up in /nix/store (world-readable[^5]) ^6 ^7. So, you should use git with flakes that way only commited files will end up in /nix/store(world-readable).

[^5]: By world-readable, I mean any service or program can access those files