When Bench is installed and the Bench Dashboard is poped up, it is time to select and install the apps you want to use. Open the Setup Window, if not allready open, and take a look into the App List. There are single apps and app groups listed.
To activate an app or a group, just check the box in the column Active. You can observe, that some boxes are in the third state, meaning, they are neither checked nor not checked. These apps are activated implicitly as a dependency of Bench or another activated app.
To start the download and installation of all activated apps,
just click on the Auto Setup Button 
in the top on the right side.
After the setup process has finished, you can close the setup window.
You can find a more detailed description of the app management in the tutorials Selecting and Installing Apps and Defining Custom Apps.