diff --git a/src/gui/main_window.py b/src/gui/main_window.py
index 1b44d06..aec4e3a 100644
--- a/src/gui/main_window.py
+++ b/src/gui/main_window.py
@@ -101,39 +101,68 @@ class MainWindow(ctk.CTk):
     # ── Config ─────────────────────────────────────────────────
 
     def _find_config(self) -> Path | None:
-        """Find the configuration file.
+        """Find the user configuration file.
 
         Checks common locations:
-        1. config/default_config.yaml (relative to app)
-        2. config/zynq_flasher.yaml
+        1. config/config.yaml (user's config)
+        2. config/default_config.yaml (template, not for saving)
         3. User-specified path via env var
 
         Returns:
-            Path to config file, or None if not found.
+            Path to user config file, or None if not found.
         """
-        candidates = [
-            Path(__file__).parent.parent / "config" / "default_config.yaml",
-        ]
+        app_dir = Path(__file__).parent.parent
+        config_dir = app_dir / "config"
 
+        # 1. Check for user config first
+        user_config = config_dir / "config.yaml"
+        if user_config.exists():
+            return user_config
+
+        # 2. Check for default config (template)
+        default_config = config_dir / "default_config.yaml"
+        if default_config.exists():
+            return default_config
+
+        # 3. Check env var
         env_path = os.environ.get("ZYNQ_CONFIG")
         if env_path:
-            candidates.insert(0, Path(env_path))
-
-        for path in candidates:
-            if path.exists():
-                return path
+            return Path(env_path)
 
         return None
 
+    def _get_user_config_path(self) -> Path:
+        """Get the path to the user config file (config.yaml).
+
+        Creates config.yaml if it doesn't exist.
+
+        Returns:
+            Path to user config file.
+        """
+        app_dir = Path(__file__).parent.parent
+        config_path = app_dir / "config" / "config.yaml"
+        config_path.parent.mkdir(parents=True, exist_ok=True)
+        return config_path
+
     def _load_config(self) -> None:
         """Load configuration from file or create default."""
         if self._config_path:
             try:
                 self._config = Config.from_file(self._config_path)
+                # If loaded from default_config.yaml, set save path to config.yaml
+                if self._config_path.name == "default_config.yaml":
+                    user_config_path = self._get_user_config_path()
+                    self._config._config_path = user_config_path
             except Exception:
                 self._config = Config.from_default()
+                # Set save path to config.yaml for new configs
+                user_config_path = self._get_user_config_path()
+                self._config._config_path = user_config_path
         else:
             self._config = Config.from_default()
+            # Set save path to config.yaml for new configs
+            user_config_path = self._get_user_config_path()
+            self._config._config_path = user_config_path
 
     def _sync_config_from_ui(self) -> None:
         """Read current UI values and update the Config object.
@@ -156,10 +185,25 @@ class MainWindow(ctk.CTk):
         self._config.firmware_bin_path = files["firmware_bin_path"]
 
     def _save_config(self) -> None:
-        """Save current configuration to file."""
+        """Save current configuration to user config file (config.yaml).
+
+        Always saves to config/config.yaml, not to default_config.yaml.
+        """
         self._sync_config_from_ui()  # Sync UI values first
-        if self._config and self._config.config_path:
+        if not self._config:
+            self._log_message("  No config loaded")
+            return
+
+        # Save to user config file (config.yaml)
+        user_config_path = self._get_user_config_path()
+        self._config._config_path = user_config_path  # Set save path
+        try:
             self._config.save()
+            self._log_message(f"  Config saved to {user_config_path}")
+            self._status.set_status("Config saved", "success")
+        except Exception as e:
+            self._log_message(f"  ✗ Save failed: {e}")
+            self._status.set_status(f"Save failed: {e}", "error")
 
     # ── UI Construction ────────────────────────────────────────
 
@@ -978,6 +1022,9 @@ class MainWindow(ctk.CTk):
         """Handle window close event: save config and cleanup."""
         if self._config:
             self._sync_config_from_ui()  # Sync UI values first
+            # Save to user config file (config.yaml)
+            user_config_path = self._get_user_config_path()
+            self._config._config_path = user_config_path
             try:
                 self._config.save()
             except Exception: