Deploy a Certificate by Using the Command Prompt

http://technet.microsoft.com/en-us/library/cc732061(WS.10).aspx

If the certificate is self-signed, and cannot be traced back to a certificate that is in your Trusted Root Certification Authorities, then you must place a copy of your certificate in that store as well.

certmgr.exe -add MyCert.cer -s -r localMachine root