Yes, as it's explained here You will have multiple nodes configured as a Replicaset with one Primary Node and 1 or more secondary nodes (up to 49 where only 7 of them can be voting members). You also may add arbiter nodes which is used whereas the primary node may step down and become a secondary and a secondary may become the primary during an election.
I am afraid we do not provide those tools. You will be able to use the Monitoring tools that Azure provides you for each of the VMs.
As you mentioned, you are the one with SSH access and, therefore, the responsible of upgrading MongoDB on your cluster. However, since we publish a new version of the Multi Tier solution whenever a new version of MongoDB is released, you could simply launch a new cluster, migrate the data from the old cluster to the new one and remove the old cluster.
You have more information about the MongoDB Multi Tier soultion on the link below:
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