The left navigation panel is usually visible in the VSys window, but the links shown in the panel change depending where you are in the system. The task panels on the right are drop-down panels that are either open or closed. When a panel is closed, you only see the title bar of the panel. To open the panel, click the title. To close a panel, click the title again.
Many tasks begin by opening a panel, and then clicking a link on the open panel. Some of the steps in the tasks involve clicking a link on the left navigation panel. When you are viewing data specific to a project or a person, the other panels are updated to only contain links, tools, and controls that are relevant to that project or that person.
In some places, like the Profile Editor, VSys hides entire panels (e.g. Mandates) if they have no content yet. You'll still see the link for the panel on the left, and clicking on that link will prompt you to add an item to that panel, after which the panel will be displayed.