You enter the port number against the 'LDAP Server' field of each TCT device you create per iPhone. The admin guide says:
For the LDAP server, enter the hostname or IP address and port of your
Active Directory server. Global catalog must be enabled, so use port
3269 for secure (SSL) connections and 3268 for nonsecure connections.
Use the format YourDirectoryServer.YourCompany.com:portnumber
.
By default, if you enter no port or SSL settings, Cisco Mobile attempts an SSL connection to port 3269.