First thing you need to do is make sure Certificate Services component of windows server is installed. This allows creation of certificates for servers. I believe one server has to be the certificate authority.
Start->Add/Remove Programs->Add/Remove Windows Components->Check Certificate Services
First start with a root authority.
Then once this is installed, you can make certificates for individual servers.
Start->Administrative Tools->Internet Information Services (IIS) Manager
Right click a website, and click properties.
Directory Services Tab->Secure Communications
Once that is done, you need to use the Root CA to accept the certificate request.
Go to http://server/certsrv you can have the certificate accepted by the Root CA