Once you have installed Shibboleth, you need to configure it to protect different areas of your site.
Simple Content Protection Examples
Protection is configured on a per-directory basis. In Apache 2.3 and earlier and Apache 2.4 on Linux this can be done using the /etc/httpd/conf.d/shib.conf file, in IIS/Windows it must be done in the C:\opt\shibboleth\etc\shibboleth\shibboleth2.xml file.
External Content Protection Documentation
A guide to all the Shibboleth options regarding content protection can be found on the Internet2 website (external).