Personally I just put all my packages in configuration.nix (well, broken up into different files but all in environment.systemPackages). I only use home manager for extra config options for programs like Git, Neovim, or VSCodium. I only have one user so I see no reason for me to separate them.
I never use the flakes search, if I find a flake on github or somewhere then it will say how to add it as a flake input and enable it. That's mostly for extra modules or things like beta versions of software that haven't been added to the official repos yet, almost all of my packages are from the standard packages.
Yeah, and I have home-manager as the nixos module, not standalone. My config is here if you were interested. Some of it is a little messy but it's pretty good.