I don't see anything in your goals that would really require flakes or home manager. Maybe the podman containers, there seem to be some sharp edges around NixOS support for podman from what I can tell.

You might not want to share your entire config but you could share snippets of what you're trying to do and isn't working.

Moving on to more concrete suggestions:

If you aren't already doing so, you should be using the option search liberally. And you should also read the code of the modules and packages, at least sometimes. Sorry, I know nixpkgs Nix can be quite obtuse, but honestly without it I don't think it's possible to really grok how NixOS works.

Secondly, a lot of people seem to think you need flakes to configure multiple systems in one repo, but you can actually also do that just fine with stable nix using the -I flag. It's even possible to build an arbitrary Nix expression using the (unfortunately undocumented) -f and -A flags like flakes would.

Edit: For secrets, I would recommend using agenix, mostly just because it uses SSH instead of GPG. Instead you can also put them in a separate Nix file and gitignore that, but your secrets will end up in /nix/store that way which is a vulnerability if they're important (also Flakes also break this completely).