Change primary/secondary link rendering and move secondary menu to footer

The configuration of the secondary menu is pretty confusing in D6. But the default setup for the secondary menu is for it to be a separate menu from the primary links menu.

So Zen 6.x-2.x’s default placement of the secondary menu should reflect the default configuration of that menu. This was the argument used in D7 to move that variable to the footer; we should do the same.