If you are looking at setting up your System Center Configuration Manager (SCCM) with PKI, then there is an excellent step by step guide that you can follow from SCCMGuy.
The link to this guide is below:
PKI Certificates for Configuration Manager 2012 R2 – Part 1 of 4 (Web Server Certificate)
We have used this in the past our various labs and it details well what you need to do.
