In the manifest project's project.config in refs/meta/config, set the following:

[plugin "manifest-subscription"]
  store = "repo/name/on/the/server"
  branch = "branch-being-monitored-in-this-repo"
  branch = "another-branch-being-monitored-in-this-repo"
  branch = "master"

There should be only one value for store. More than one value for branch.