When using an internal Microsoft Certificate Authority, there was a small gotcha installing an SSL certificate on the PRTG web interface.
Use this article in order to install the SSL certificate on the PRTG server. You will also need OpenSSL installed on a machine as well:
There is only ONE thing to note on this procedure. The COMMON NAME you give the certificate during the OpenSSL process is apparently not used at all with PRTG. So you will want to add ALL the Subject Alternative Names in the additional attributes portion of the request in IIS on CertSrv including the primary name you might use to access the server's web interface.
For example, on a server named PRTG1 you would included all these SANs:
Which Translates to the following in the SAN portion of the cert:
This allows us to hit PRTG from any of those names without a certificate warning.