diff --git a/CodeEntropy/config/arg_config_manager.py b/CodeEntropy/config/arg_config_manager.py
index 5908326..cacb73a 100644
--- a/CodeEntropy/config/arg_config_manager.py
+++ b/CodeEntropy/config/arg_config_manager.py
@@ -101,19 +101,32 @@ def merge_configs(self, args, run_config):
         if not isinstance(run_config, dict):
             raise TypeError("run_config must be a dictionary or None.")
 
-        # Step 1: Merge YAML configuration into args
-        for key, value in run_config.items():
-            if getattr(args, key, None) is None:
-                setattr(args, key, value)
+        # Convert argparse Namespace to dictionary
+        args_dict = vars(args)
+
+        # Reconstruct parser and check which arguments were explicitly provided via CLI
+        parser = self.setup_argparse()
+        default_args = parser.parse_args([])
+        default_dict = vars(default_args)
+
+        cli_provided_args = {
+            key for key, value in args_dict.items() if value != default_dict.get(key)
+        }
+
+        # Step 1: Apply YAML values if CLI didn't explicitly set the argument
+        for key, yaml_value in run_config.items():
+            if yaml_value is not None and key not in cli_provided_args:
+                logger.debug(f"Using YAML value for {key}: {yaml_value}")
+                setattr(args, key, yaml_value)
 
-        # Step 2: Set default values for any missing arguments from `arg_map`
+        # Step 2: Ensure all arguments have at least their default values
         for key, params in self.arg_map.items():
             if getattr(args, key, None) is None:
                 setattr(args, key, params.get("default"))
 
-        # Step 3: Override with CLI values if provided
+        # Step 3: Ensure CLI arguments always take precedence
         for key in self.arg_map.keys():
-            cli_value = getattr(args, key, None)
+            cli_value = args_dict.get(key)
             if cli_value is not None:
                 run_config[key] = cli_value