You've probably resolved this, and I'm not 100% sure I understand your query, but I think Widget Logic plugin may be what you're looking for http://wordpress.org/extend/plugins/widget-logic/
It will allow you to have the Flexipages widget only display on certain pages. Then you can create another Flexipages widget and have that display on other pages. Thus allowing you to have a variety of different sidebar menus appear depending on the page you're on.