We now have a much easier editor for your linkbar. Click for more information.
Our old linkbar editor used a confusing file-manager-like tree, with draggable unused links. We've redesigned it with a much cleaner interface. From the "Linkbar" item of your site's "Content" menu, just click and drag the links around to move them. Drag them to the right, and you can easily nest them below top-level links. A new warning will tell you if you've overflowed the available space.
To add links, just click the "Add New Link" button. The page gives you a tree of most of the linkable pages of your site. Select the link you'd like to use, and click the "Add Link" button to add it to the end of your linkbar. You can also click the "Create Custom Link" to link to a page not listed in the tree, or the "Create New Page" button to make a new page from scratch.