do you have to run most of these things through command prompt
That would depend on the type of application. If it has a GUI, then yes, you can access it from the menus or even add a link/launcher on your panel(s) or the desktop.
As for adding stuff to the menu / desktop, the location needs to be the full path to the application in question. For example: /usr/bin/firefox. However, you also have a PATH on your system that will automatically search a number of folders. You can see the path by becoming root and typing:
This will show that /usr/bin is in your PATH; as a consequence, all applications located there can be started by using just their name, without the rest of the path. The system will be able to find them by going over the list of the directories in its PATH variable. Thus the command firefox works just as well as /usr/bin/firefox.
Oh yes, and another note, if you are going to edit/add menu items or launchers, you may find that the system can't find an icon. Just browse to /usr/share/pixmaps. You can also create your own icons and add them to that folder first (or to any other one for that matter).