I know that the plans for Hierarchical Menu include allowing multiple menus (but he hasn't made a new release yet).
In the mean time I've been thinking it might be possible by using Container/Containable parts to create a couple of menu lists. You can use Container Widget to add your menus to the appropriate layout zones, and override templates so you get menu-friendly
If you use Page as your Containable then you'd have the disadvantage that you can only add any particular page into one menu. However if you create a custom type called "Menu Link" and give it custom fields of URL and caption, you could construct menus in
any way you wished. Of course it would require manually adding everything to the menu since the "Show in main menu" tick box wouldn't apply. Maybe you could stick with the Navigation top menu, and use your custom list just for a footer menu which might not
There are probably a load of other ways around this problem!