No clue about “proper”, but this is what I do:

https://github.com/Ajlow2000/home-manager/blob/main/users/ajlow.nix#L96

Basically just symlinking. For now I prefer configuring various tooling in the native style and then just symlinking the config files to where they should end up.

Providing some links on flakes:

The wiki is a solid starting point: https://nixos.wiki/wiki/Flakes

This video: https://youtu.be/S3VBi6kHw5c?si=oC0zXzQ8XWTCqM-y

Side note. Vimjoyer on YouTube (that video link above) is pretty solid. I like his content/tutorials a lot