Where exactly do I add this? I added it to the modules but that returned an error.

....
nixosConfigurations = {
  nixos = nixpkgs.lib.nixosSystem {
    specialArgs = ....
    system = ....
    modules = [
    ]
.......
.....

outputs = { self, nixpkgs, nixpkgs-unstable }@inputs: 
  let
    system = "x86_64-linux";
    specialArgs = inputs // { inherit system; };
  in
  {
    nixosConfigurations = {
      audioproc1 = nixpkgs.lib.nixosSystem {
        specialArgs = specialArgs;
        system = system;
        modules = [ 
          ./hosts/audioproc1/configuration.nix
          ./nixosModules
          { packages.${system}.stereo_tool_gui_jack_64 = nixpkgs.legacyPackages.${system}.callPackage ./packages/stereo_tool_gui_jack_64.nix {}; }
        ];
      };
    };
  };

I did this, but I get an error that "packages" does not exist.

I did this:

preFixup = let
    libPath = lib.makeLibraryPath [
      xorg.libX11
      xorg.libXpm
      alsa-lib
      zlib
    ];
    in ''
      patchelf --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
        --set-rpath "${libPath}" $out/bin/stereo_tool_gui_jack_64
    '';

But I'm getting an error of "No such file or directory"

It produces the following, which has a prefix for the file name.

and in the patchelf I'm referencing $out/bin/stereo_tool_gui_jack_64.

So I think there is a mismatch happening there.

I did this:

preFixup = let
    libPath = lib.makeLibraryPath [
      xorg.libX11
      xorg.libXpm
      alsa-lib
      zlib
    ];
    in ''
      patchelf --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
        --set-rpath "${libPath}" $out/bin/stereo_tool_gui_jack_64
    '';

But I'm getting an error of "No such file or directory"

It produces the following, which has a prefix for the file name.

nix/store/1rfxwagch6q2xsx6si07rw2sm0lgn1wy-stereo_tool_gui_jack_64-v10.30/bin/xn02wh7bk6fww0l9kpnn4mbmgx4505by-stereo_tool_gui_jack_64

and in the patchelf I'm referencing $out/bin/stereo_tool_gui_jack_64.

So I think there is a mismatch happening there.

Running phase: fixupPhase
patchelf: getting info about '/nix/store/1rfxwagch6q2xsx6si07rw2sm0lgn1wy-stereo_tool_gui_jack_64-v10.30/bin/stereo_tool_gui_jack_64': No such file or directory

almost there..... now you use an overlay to add your package to the "pkgs" available in your NixOS config.... something close to this:

 nixosConfigurations = {
      audioproc1 = nixpkgs.lib.nixosSystem {
        specialArgs = specialArgs;
        system = system;
        modules = [
          {
            nixpkgs.overlays = [(final: prev: {
              inherit (self.packages.${system}) stereo_tool_gui_jack_64;
           })];
          }
          ./hosts/audioproc1/configuration.nix
          ./nixosModules
        ];
      };
    };