I’m hoping you’ve since gotten past the installation guide issue you describe above, however, for reference, you can install the Server (as well as other components) by accessing the setup files under the BES Installers folder (by default under: C:\Program Files (x86)\BigFix Enterprise\BES Installers). So, for instance, for the BigFix Server, the setup executable would be at the following location by default on Windows:
C:\Program Files (x86)\BigFix Enterprise\BES Installers\Server\setup.exe