In the GateIn, there is a horizontal admin toolbar on the top of page where is starting point of management ( make sure that you are one of administrators ).
To manage navigation for :
+ Portal : click on the Site link to show the Site Navigation portlet. In here, there is a Create Portal button too
+ Group : click on the Group link to show the Group Navigation portlet
Yes, agreed it's not intuitive
Temporarily there is one thing you can do if you want is to create a node "Manage portal" which points to the page containing the Portal Navigation portlet.