Sergio wrote: checkboxes in your story settings window...check-all and uncheck-all button...
The concept sounds simple and flexible.
However try this, click on your marquee tool and notice that big empty Info Box.
Wouldn't it be better to have a Story List and Check Box interface appear in this palette? Avoiding a trip to the Story Settings dialog box.
The list showing the User defined names of the stories, not simply the generic number/story routine.
You also said "walls" in your comment. It makes me wonder if there should also be a check box interface similar to the story dialog boxes copy/paste so one could determine which items are affected with having to lock or turn off layers.
Then I suppose there is value in being able to save named sets of what is checked for various situations.