Here is how I figured out how to add databases so we could enable replication. Will allow you to set bundles.
  public static void EnsureDatabaseExists(string dbname, string primaryUrl, string replicationUrl)
    {
      using (var store = new DocumentStore { Url = primaryUrl, DefaultDatabase = null })
      {
        store.Initialize();
        var serverClient = (ServerClient)store.DatabaseCommands.ForSystemDatabase();
        try
        {
          //if exists, return
          if (serverClient.Get("Raven/Databases/" + dbname) != null)
          {
            return;
          }
        }
        catch (Exception ex)
        {
          ex.SendToStackify();
          return;
        }
        //We have to do this so we can specify the bundles we need to enable replication.
        //The built in EnsureDatabase method won't enable replication
        DatabaseDocument newDB = new DatabaseDocument()
          {
            Settings =
              {
                {"Raven/DataDir", Path.Combine("~", Path.Combine("Databases", dbname))},
                {"Raven/ActiveBundles", "PeriodicBackup;Replication"}
              }
          };
        Â
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        var docNew = RavenJObject.FromObject(newDB);
        docNew.Remove("Id");
        try
        {
          var req = serverClient.CreateRequest("PUT", "/admin/databases/" + Uri.EscapeDataString(dbname));
          req.Write(docNew.ToString(Formatting.Indented));
          req.ExecuteRequest();
        }
        catch (Exception ex)
        {
          ex.SendToStackify();
        }
        //Create the standard index
        try
        {
          new RavenDocumentsByEntityName().Execute(serverClient.ForDatabase(dbname), new DocumentConvention());
        }
        catch (Exception ex)
        {
          ex.SendToStackify();
        }
        if (replicationUrl != null)
        {
          ReplicationDocument replicationDocument = new ReplicationDocument();
          ReplicationDestination destination = new ReplicationDestination()
            {
              Url = replicationUrl,
              Database = dbname,
              TransitiveReplicationBehavior = TransitiveReplicationOptions.None,
              IgnoredClient = false,
              Disabled = false
            };
          replicationDocument.Destinations.Add(destination);
          using (var session = store.OpenSession(dbname))
          {
            session.Store(replicationDocument, replicationDocument.Id);
            session.SaveChanges();
          }
        }
      }
    }