addyall: If you are just trying to create a menufile for yourself then by all means go ahead. I just want you to be aware of the reason we dropped flux box. KDE and gnome and certain other window managers are what is called free desktop complaint which means they all use a tool.desktop file in their menus. This makes it very easy for a package manager to add and remove menu entries. This is not possible to do with flux box because it uses a XML type file for its menu.
As for your second question simply modify the bt3 menu. Over half the tools are in the same sections so just add the new ones.