Yes, you can import an SSL certificate and private key into ISE. Be sure you import the root CA certificate into the Trusted Certificates store first. Review the directions here, under Import a System Certificate, for more information:
Cisco ISE 1.4 Admin Guide - Managing Certificates
Are you using a wildcard? If so, the wildcard needs to be in the SAN. Use a generic name (e.g. aaa.domain.com) as the CN.