LDAP authentication between the Monitoring/Backup Agent and the MongoDBs it monitors/backs-up is very straightforward to configure. Simply choose "LDAP" as the authentication mechanism in the "Add Host", "Edit Host" (monitoring) and "Start Sync" (backup) forms.
Also, please include a trouble-shooting section that covers the following situation:
You are running MongoDB with LDAP. You forget to change "MONGODB-CR" to "LDAP (PLAIN)" since they both take username/password.
The error message from MongoDB is "Challenge-response authentication using getnonce and authenticate commands is disabled."
It would be nice to document this somewhere in an agent faq that the actual problem is that you most likely are using LDAP but selected MONGODB-CR.