Have you been defining them directly in your flake.nix file? I too am on nixos but I keep all my configurations in their native format and symlink them with nix, that way I can take and reuse that config on a non nixos system easily.

The problem I have found is that nixos doesn't seem to pickup and run systemd timers and services placed into the ~/.config/systems/user folder and additionally things like WantedBy=default.target have no effect.

So after I restart all my services manually on reboot I agree, systems timers are cool.