Prototype jobs should not contain the actual commands, notification requirements or the notes section controls for the property page display. Instead they should contain an include statement that pulls in the corresponding data from a base job. After the prototype has been used numerous times any changes to this base job will then affect all those created jobs. These base jobs should be placed in their own directory, for example /controls/.
Global prototype jobs should be placed in the folder /default/xxxx/ where xxxx is the name of your application. This will allow the New job from... menu item to be consistently displayed across the whole system.
While testing these prototypes out place them in your personal top level directory. When they work as designed move them into the global location.