Each section is automatically handled by the framework, but you can always decide to override defaults.
You can refer to myfirstpage.js file to have an idea about how to interract with the framework using jQuery.
You can easily customize the sidemenu, just update both html/sidemenu.html and js/sidemenu.js files.
Same for right usermenu, use html/usermenu.html and js/usermenu.js files.
But if you like the framework as itself and you want to keep concentrated for your own app, well you’ll just have to create a page as described in introduction section – myfirstpage -, doing that way ill automatically put you app inside IDmain part.