diff --git a/README.md b/README.md
index da9f9a4..670462a 100644
--- a/README.md
+++ b/README.md
@@ -228,6 +228,21 @@ Please [let me know](https://github.com/Misterio77/nix-starter-config/issues)
 any questions or issues you face with these templates, so I can add more info
 here!
 
+## I'm trying to set nixpkgs.config options (e.g. allowUnfree), but they won't work!
+
+We instantiate nixpkgs and pass it to NixOS, to make the flake a bit simpler
+and ensure both configs have the same nixpkgs instance, this has the drawback
+of breaking nixpkgs configuration through in your NixOS config files.
+
+This is a design choice I made based on the `homeManagerConfiguration`
+interface, that requires a `pkgs` instance anyway. If you prefer to set them
+modularly, you'll have to remove the `pkgs` argument. If you use overlays,
+you'll have to pass them into your configuration (through specialArgs) or set
+`nixpkgs.overlays` right on the flake; in this case, you might prefer to use
+[home-manager as a NixOS
+module](https://nix-community.github.io/home-manager/index.html#sec-flakes-nixos-module)
+and set `home-manager.useGlobalPkgs = true`.
+
 ## Nix says my repo files don't exist, even though they do!
 
 Nix flakes only see files that git is currently tracked, so just `git add .`
diff --git a/minimal/flake.nix b/minimal/flake.nix
index 6d98fc9..3f34bec 100644
--- a/minimal/flake.nix
+++ b/minimal/flake.nix
@@ -17,11 +17,25 @@
     # nix-colors.url = "github:misterio77/nix-colors";
   };
 
-  outputs = { nixpkgs, home-manager, ... }@inputs: {
+  outputs = { nixpkgs, home-manager, ... }@inputs: rec {
+    # This instantiates nixpkgs for each system listed
+    # Allowing you to configure it (e.g. allowUnfree)
+    # Our configurations will use these instances
+    legacyPackages = nixpkgs.lib.genAttrs [ "x86_64-linux" "x86_64-darwin" ] (system:
+      import inputs.nixpkgs {
+        inherit system;
+        # NOTE: Using `nixpkgs.config` in your NixOS config won't work
+        # Instead, you should set nixpkgs configs here
+        # (https://nixos.org/manual/nixpkgs/stable/#idm140737322551056)
+
+        # config.allowUnfree = true;
+      }
+    );
+
     nixosConfigurations = {
       # FIXME replace with your hostname
       your-hostname = nixpkgs.lib.nixosSystem {
-        pkgs = nixpkgs.legacyPackages.x86_64-linux;
+        pkgs = legacyPackages.x86_64-linux;
         specialArgs = { inherit inputs; }; # Pass flake inputs to our config
         # > Our main nixos configuration file <
         modules = [ ./nixos/configuration.nix ];
@@ -32,7 +46,7 @@
       # FIXME replace with your username@hostname
       "your-username@your-hostname" =
         home-manager.lib.homeManagerConfiguration {
-          pkgs = nixpkgs.legacyPackages.x86_64-linux;
+          pkgs = legacyPackages.x86_64-linux;
           extraSpecialArgs = { inherit inputs; }; # Pass flake inputs to our config
           # > Our main home-manager configuration file <
           modules = [ ./home-manager/home.nix ];
diff --git a/standard/flake.nix b/standard/flake.nix
index cdace3a..6d015f3 100644
--- a/standard/flake.nix
+++ b/standard/flake.nix
@@ -19,8 +19,7 @@
 
   outputs = { nixpkgs, home-manager, ... }@inputs:
     let
-      forAllSystems = nixpkgs.lib.genAttrs systems;
-      systems = [
+      forAllSystems = nixpkgs.lib.genAttrs [
         "aarch64-linux"
         "i686-linux"
         "x86_64-linux"
@@ -29,7 +28,9 @@
       ];
     in rec {
       # Your custom packages and modifications
-      overlays = { default = import ./overlay { inherit inputs; }; };
+      overlays = {
+        default = import ./overlay { inherit inputs; };
+      };
 
       # Reusable nixos modules you might want to export
       # These are usually stuff you would upstream into nixpkgs
@@ -44,13 +45,22 @@
         default = legacyPackages.${system}.callPackage ./shell.nix { };
       });
 
-      # Reexport nixpkgs with our overlays applied
-      # Acessible on our configurations, and through nix build, shell, run, etc.
+      # This instantiates nixpkgs for each system listed above
+      # Allowing you to add overlays and configure it (e.g. allowUnfree)
+      # Our configurations will use these instances
+      # Your flake will also let you access your package set through nix build, shell, run, etc.
       legacyPackages = forAllSystems (system:
         import inputs.nixpkgs {
           inherit system;
+          # This adds our overlays to pkgs
           overlays = builtins.attrValues overlays;
-        });
+          # NOTE: Using `nixpkgs.config` in your NixOS config won't work
+          # Instead, you should set nixpkgs configs here
+          # (https://nixos.org/manual/nixpkgs/stable/#idm140737322551056)
+
+          # config.allowUnfree = true;
+        }
+      );
 
       nixosConfigurations = {
         # FIXME replace with your hostname