How to associate a node with a menu without adding it to the menu
I am not exactly sure of what you are trying to accomplish here, but it sounds like you are trying to use menus to alter the breadcrumb behavior

If that's the case, you should try the menu breadcrumb module - http://drupal.org/project/menu_breadcrumb or the custom breadcrumb module - http://drupal.org/project/custom_breadcrumbs

Hope this helps