These actions are available under the Project menu, under the Soot menu item. The Soot menu item appears in the Project menu after selecting it from Window -> Customize Perspective -> Other -> Soot
If the menu items are unavailable (greyed out): Select any file in the Package Explorer (in the project you wish to work on) and try again.
You can run Soot either on all the classes in your project or all the source files. You must build the project before using Soot on class files.