Configuring Windchill with Multilayer certificates is pretty much the same as configuring a single certificate. It just we need to understand why this is needed.
Many companies who issue certificates provide multilayer certificates. These are also called as chained certificates. A multilayer certificate is a combination of a primary certificate and an intermediate certificate. An intermediate certificate is a subordinate certificate issued by the trusted root specifically to issue end-entity server certificates. The result is a certificate chain that begins at the trusted root CA, through the intermediate and ending with the SSL certificate issued to you. Such certificates are called chained root certificates.
In chained certificates you have to install 2 certificates the intermediate and the primary certificate. All you need to do is follow the same procedure in my Previous topic(Windchill with HTTPS) once for intermediate and once for the primary certificate.
This is how an intermediate certificate from Verisign looks:
Once you have this installed then you need to import the primary certificate. After you import the intermediate and primary certificate, this is how your certificate looks like when you open the primary certificate obtained from Windchill
If it is not installed properly many Windchill Modules such as Publishing, PSE etc. stop working.