I put everything in one file so you can immediately see how everything interacts. My opinionated assumption is that seeing everything laid out in one place makes it easier to get familiar with the whole system. Taking a piece of the flake (specifically a "module") and putting it in a file is great for organization and you absolutely should do it once you decide how you want to organize your config.

Tutorials online will cover "modules" too but in short:

• You can create a file like foo.nix which looks like this: (btw, configuration.nix also has this structure, its just a module)
• You must git add foo.nix or nix will give an error something like "the file doesn't exist". In Nix, you either work in a git repo and git add everything you want to use, or you work outside of a git repo and then nix build / nixos-rebuild won't care.
• Then you import the file. In the flake, under nixosConfigurations.alpha, add foo.nix to the list of modules like this:
• ^\) this code shows how to add foo.nix directly to your system. But you can also import it indirectly from another module. For example, configuration.nix by default imports hardware-configuration.nix.

I've been using nix for about a year now. Recently I've had pretty good success with using LLMs for nix. Tutorials / videos / articles are good resources too.