Hello Ewout,
I am using the free version, and only added the Menu Cart to the left sidebar menu as a way to show that it works on some aspects. In WP Symposium Toolbar you create menus and then assign them to positions on the toolbar. For instance, on the right side of the toolbar the “Sign Up” item is actually an individual custom menu called “WPS Login” and the “Register” link is a menu called “Register”.
The only thing I can think of is that the theme I am using only has one menu location called “header menu” which is what you see on the left. If you need to see the backend I can e-mail the credentials (it is a staging site anyway).
Sartorius