We have our own mongo replica set setup in aws ec2, it is running all good. Now, what we want is to get MMS setup to monitor and backup the replica set. It seems that MMS will only monitor and backup the mongo instance that was deployed by the MMS.
Is there a work around for this?
As of the mid-October 2014 release of MMS, monitoring & backup has been integrated with deployment via the automation agent (http://blog.mongodb.org/post/99991498968/mongodb-management-service-re-imagined-the-easiest-way). There currently isn't an option to attach MMS to existing MongoDB deployments, however you can watch/upvote MMS-1991 in the MongoDB issue tracker for updates.
Is there a work around for this?
One option would be to deploy a new replica set using MMS and migrate your data to the managed deployment.
If you have an MMS group created with the pre-automation version, the "classic" MMS groups do not have support for automation and the agents can be installed independently. Note that the classic version of MMS is closed to new users.