Every tool has a "Configure" link in the main toolbar that is only visable to administrators who are logged in. Within this section, there are several subsections (some tools have more than others). By clicking on the subsection header, the subsection will expand and display the options.
This section of the documentation covers each universal subsection in detail. Some of the subsections such as "Tool Setup" are specific to the tool, and covered in detail in that tool's section of the documentation.