Yes I’m using flakes and loving them. my user pkg’s are managed through home-manager’s nixos module so i would think my user channel would track the inputs of my flake i.e master. the fact that my channels lag behind is annoying part I’m not actually sure what all uses the channels.
For flakes, I simply pin nix.nixPath = [ "nixpkgs=${inputs.nixpkgs}" ], where inputs are your system’s flake inputs. That way, legacy commands and flake based commands use the same underlying nixpkgs source. One could then simply not bother with channels at all at that point.