The menu has two ways of displaying the programs, as a drop-down list and the tree-structure menu. To get the tree-structure, go to options and select use tree menu. Once this is selected, two additional features underneath will be highlighted Hide Menu window and Save Window Position. The first feature, as it name says, will allow you to hide the window while you are working with one of the programs. The second one will keep the position of the window. Next time that you open your menu and select one of the modules, you will get the window in the position that you selected before.
This is a view of the tree-structure