diff --git a/Gemfile.lock b/Gemfile.lock
index a968d18..f0ce4fb 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -2,6 +2,7 @@ PATH
   remote: .
   specs:
     configman (1.0.0)
+      deep_dup
       inifile
 
 GEM
@@ -9,6 +10,7 @@ GEM
   specs:
     ast (2.4.2)
     base64 (0.1.1)
+    deep_dup (0.0.3)
     diff-lcs (1.5.0)
     inifile (3.0.0)
     json (2.6.3)
diff --git a/configman.gemspec b/configman.gemspec
index 6eca2d7..c7ffabc 100644
--- a/configman.gemspec
+++ b/configman.gemspec
@@ -28,6 +28,7 @@ Gem::Specification.new do |spec|
 
   # Uncomment to register a new dependency of your gem
   # spec.add_dependency "example-gem", "~> 1.0"
+  spec.add_dependency 'deep_dup'
   spec.add_dependency 'inifile'
 
   # For more information and examples about making a new gem, check out our
diff --git a/lib/configman.rb b/lib/configman.rb
index 2f68eaf..ed2ea8a 100644
--- a/lib/configman.rb
+++ b/lib/configman.rb
@@ -14,6 +14,20 @@ module ConfigMan
   @loaded_parser = nil
   @custom_modules = []
 
+  EXPECTED_KEYS = {
+    'API' => %w[api_endpoint api_key rate_limit],
+    'Cache' => %w[cache_type host port],
+    'Database' => %w[db_host db_port db_user db_password db_name],
+    'Email' => %w[smtp_server smtp_port smtp_user smtp_password smtp_protocol],
+    'FileStorage' => %w[storage_type cloud_provider local_path],
+    'Localization' => %w[language time_zone encoding],
+    'Logging' => %w[log_level log_file log_rotation]
+  }.freeze
+
+  def self.expected_keys
+    EXPECTED_KEYS
+  end
+
   # register any custom modules the user provides
   def self.register_module(file_path)
     raise ArgumentError, "File not found: #{file_path}" unless File.exist?(file_path)
@@ -30,13 +44,23 @@ module ConfigMan
     @custom_modules << mod_class
   end
 
+  def self.used_modules
+    @used_modules
+  end
+
   # Setup ConfigMan with presets
   def self.setup(default_modules, custom_options = {})
+    # Check if a parser is loaded
+    raise 'No parser module loaded. Please load a parser module before calling setup.' if @loaded_parser.nil?
+
     final_config = {}
 
+    # Remove parser names from default_modules
+    default_modules = default_modules.reject { |mod| %w[json ini xml yaml].include?(mod.downcase) }
+
     # Populate defaults from built-in modules
     default_modules.each do |mod|
-      mod_class = Object.const_get("ConfigMan::Modules::#{mod.capitalize}")
+      mod_class = Object.const_get("ConfigMan::Modules::#{mod}")
       final_config.merge!(mod_class.populate_defaults)
     end
 
@@ -85,6 +109,7 @@ module ConfigMan
       if %w[json ini xml yaml].include?(module_name.downcase)
         # It's a parser
         require_relative "configman/parsers/#{module_name.downcase}"
+        @loaded_parser = module_name.downcase
       else
         # It's a regular module
         require_relative "configman/modules/#{module_name.downcase}"
diff --git a/lib/configman/modules/api.rb b/lib/configman/modules/api.rb
index 76f6b07..78ed421 100644
--- a/lib/configman/modules/api.rb
+++ b/lib/configman/modules/api.rb
@@ -2,7 +2,7 @@
 
 module ConfigMan
   module Modules
-    module Api
+    module API
       def self.populate_defaults
         {
           'api_endpoint' => 'https://api.example.com',
diff --git a/lib/configman/modules/localization.rb b/lib/configman/modules/localization.rb
index f074984..cd5e2d6 100644
--- a/lib/configman/modules/localization.rb
+++ b/lib/configman/modules/localization.rb
@@ -6,7 +6,8 @@ module ConfigMan
       def self.populate_defaults
         {
           'language' => 'en',
-          'time_zone' => 'UTC'
+          'time_zone' => 'UTC',
+          'encoding' => 'UTF-8'
         }
       end
     end
diff --git a/lib/configman/modules/utils.rb b/lib/configman/modules/utils.rb
new file mode 100644
index 0000000..c3a7795
--- /dev/null
+++ b/lib/configman/modules/utils.rb
@@ -0,0 +1,29 @@
+# frozen_string_literal: true
+
+# config_util.rb
+
+module ConfigMan
+  module Utils
+    def self.sort_into_sections(config_hash, expected_keys, loaded_modules)
+      sorted_config = Hash.new { |hash, key| hash[key] = {} }
+
+      config_hash.each do |key, value|
+        section_found = false
+
+        expected_keys.each do |section, keys|
+          next unless loaded_modules.include?(section)
+
+          next unless keys.include?(key)
+
+          sorted_config[section][key] = value
+          section_found = true
+          break
+        end
+
+        sorted_config['General'][key] = value unless section_found
+      end
+
+      sorted_config
+    end
+  end
+end
diff --git a/lib/configman/parsers/ini.rb b/lib/configman/parsers/ini.rb
index 6722c7e..1960cda 100644
--- a/lib/configman/parsers/ini.rb
+++ b/lib/configman/parsers/ini.rb
@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 require 'inifile'
+require_relative '../modules/utils'
 
 module ConfigMan
   module Parsers
@@ -30,7 +31,19 @@ module ConfigMan
       end
 
       def self.write(config_hash)
-        ini = IniFile.new(content: config_hash)
+        # Access the loaded modules and expected keys from the main class
+        loaded_modules = ConfigMan.used_modules
+        expected_keys = ConfigMan.expected_keys
+
+        # Sort the keys into their respective sections
+        sorted_config = Utils.sort_into_sections(config_hash, expected_keys, loaded_modules)
+
+        # Debug statement to output the sorted_config
+        puts 'Debug: About to write the following sorted_config to INI file:'
+        p sorted_config
+
+        # Write the sorted config to the INI file
+        ini = IniFile.new(content: sorted_config)
         ini.write(filename: CONFIG_FILE_PATH)
       end
     end
diff --git a/lib/configman/parsers/json.rb b/lib/configman/parsers/json.rb
index 4762d46..9ae1594 100644
--- a/lib/configman/parsers/json.rb
+++ b/lib/configman/parsers/json.rb
@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 require 'json'
+require_relative '../modules/utils'
 
 module ConfigMan
   module Parsers
@@ -11,8 +12,6 @@ module ConfigMan
       def self.parse(file_path)
         raise ArgumentError, "File not found: #{file_path}" unless File.exist?(file_path)
 
-        @file_path = file_path
-
         file_content = File.read(file_path)
         parsed_config = ::JSON.parse(file_content)
 
@@ -22,21 +21,24 @@ module ConfigMan
       end
 
       def self.update(key, new_value)
-        # Read existing config
-        existing_config = parse
-
-        # Update the value
+        existing_config = parse(CONFIG_FILE_PATH)
         existing_config[key] = new_value
 
-        # Write the updated config back to the file
         File.open(CONFIG_FILE_PATH, 'w') do |file|
           file.write(::JSON.pretty_generate(existing_config))
         end
       end
 
       def self.write(config_hash)
+        # Access the loaded modules and expected keys from the main class
+        loaded_modules = ConfigMan.used_modules
+        expected_keys = ConfigMan.expected_keys
+
+        # Use the utility method to sort the keys into their respective sections
+        sorted_config = Utils.sort_into_sections(config_hash, expected_keys, loaded_modules)
+
         File.open(CONFIG_FILE_PATH, 'w') do |file|
-          file.write(::JSON.pretty_generate(config_hash))
+          file.write(::JSON.pretty_generate(sorted_config))
         end
       end
     end
diff --git a/lib/configman/parsers/xml.rb b/lib/configman/parsers/xml.rb
index 0c2acab..5637892 100644
--- a/lib/configman/parsers/xml.rb
+++ b/lib/configman/parsers/xml.rb
@@ -1,6 +1,8 @@
 # frozen_string_literal: true
 
 require 'rexml/document'
+require 'rexml/formatters/pretty'
+require_relative '../modules/utils'
 
 module ConfigMan
   module Parsers
@@ -32,15 +34,32 @@ module ConfigMan
         doc.add_element('config')
         existing_config.each { |k, v| doc.root.add_element(k).text = v }
 
-        File.open(CONFIG_FILE_PATH, 'w') { |file| doc.write(file) }
+        formatter = REXML::Formatters::Pretty.new
+        File.open(CONFIG_FILE_PATH, 'w') do |file|
+          formatter.write(doc, file)
+        end
       end
 
       def self.write(config_hash)
+        # Access the loaded modules and expected keys from the main class
+        loaded_modules = ConfigMan.used_modules
+        expected_keys = ConfigMan.expected_keys
+
+        # Sort the keys into their respective sections
+        sorted_config = Utils.sort_into_sections(config_hash, expected_keys, loaded_modules)
+
         doc = REXML::Document.new
         doc.add_element('config')
-        config_hash.each { |k, v| doc.root.add_element(k).text = v }
 
-        File.open(CONFIG_FILE_PATH, 'w') { |file| doc.write(file) }
+        sorted_config.each do |section, section_data|
+          section_element = doc.root.add_element(section)
+          section_data.each { |k, v| section_element.add_element(k).text = v }
+        end
+
+        formatter = REXML::Formatters::Pretty.new
+        File.open(CONFIG_FILE_PATH, 'w') do |file|
+          formatter.write(doc, file)
+        end
       end
     end
   end
diff --git a/lib/configman/parsers/yaml.rb b/lib/configman/parsers/yaml.rb
index ac3f85a..ec41f45 100644
--- a/lib/configman/parsers/yaml.rb
+++ b/lib/configman/parsers/yaml.rb
@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 require 'yaml'
+require_relative '../modules/utils'
 
 module ConfigMan
   module Parsers
@@ -28,8 +29,15 @@ module ConfigMan
       end
 
       def self.write(config_hash)
+        # Access the loaded modules and expected keys from the main class
+        loaded_modules = ConfigMan.used_modules
+        expected_keys = ConfigMan.expected_keys
+
+        # Use the utility method to sort the keys into their respective sections
+        sorted_config = Utils.sort_into_sections(config_hash, expected_keys, loaded_modules)
+
         File.open(CONFIG_FILE_PATH, 'w') do |file|
-          file.write(config_hash.to_yaml)
+          file.write(sorted_config.to_yaml)
         end
       end
     end