Hi, the Controls Window shows a window in each scene that tells the player what buttons to press, and can detect if the last input was a keyboard or a controller and change the instructions accordingly. You can see a gif preview of it on this page.
For adding things to the main menu, you would use [CGMZ] Menu Command Window. To add a custom command with that plugin, such as for achievements or encyclopedia, you would open that plugin in the Plugin Manager and double click on the Commands parameter. You will see a list of commands where you can enter new commands.
To get a menu entry that says "Achievements" and leads to the achievements scene: For the Command Name, put "Achievements". For the Command Symbol, put "achievements", for the JS Command parameter put
SceneManager.push(CGMZ_Scene_Achievements);
To get a menu entry that says "Encyclopedia" and leads to the encyclopedia scene: For the Command Name, put "Encyclopedia". For the Command Symbol, put "encyclopedia", for the JS Command parameter put
SceneManager.push(CGMZ_Scene_Encyclopedia);