Checking or unchecking applies that action to all levels below the one you changed.
The current Workspace is shown at the top with the current Target first. Other Workspaces on your Recent list are under Recent Workspaces. All other Workspaces are under Other Workspaces. When running PBSearch against PB7 and below, it organizes your applications in a similar manner. For PB7 and below it uses the term Application instead of Workspace and uses the appropriate icons.
Whatever window is currently displayed on the right side of the window will process the libraries selected in the System Tree.
There is a vertical sizebar in-between the System Tree and the right hand side of the window. You can slide it left to right to adjust how much you can see.
Right clicking on a library displays a popup menu with the choice Properties. This displays the Library Properties window.
Right clicking on a Target displays a popup menu with Library Filter options. See the Library Filter Manager for an explanation.