You can customize the Main Window's menus and toolbars in the Global Options window -- look for the nodes for Actions (a pool of available actions), Menu (the main menu bar), and Toolbars (a list of configurable toolbars). You can use the clipboard (copy and paste) to reconfigure toolbars and menus to your taste.

You can grab toolbars by their grips and rearrange them by dragging. If you right-click on an empty space in the toolbar area, a contextual menu will appear allowing you to add or remove toolbars from the current configuration and to create new configurations.

You can also make your own menu and toolbar items. Just make a Java class with a main method to do what you want. Then set it to use Internal Execution (Executor property on the Execution tab on the source file's property sheet), and copy & paste it into a menu or toolbar in the Menu or Toolbars nodes in the Global Options window.