Need help integrating with Microsoft Certificate Services

I have searched and haven't found a solution so if I missed something please point me in the right direction.

Here is my scenario.

I have just stood up a new Encryption 3.30 server and have it setup to use auto-enrolment of users using LDAP directory sync with my two AD Domains.  We have an MS Certificate authority setup and all of or PCs trust that certificate chain.

I need to know if I can setup the Encryption server to trust the AD Certificate chain so it doesn't prompt the user to trust the Encryption servers self-generated certificate.