You're correct that you can only have either Controls or Indicators in a cluster.
You can operate on individual cluster elements regardless of which type (control or indicator) they are initially. Define your cluster with all the elements you need, pass this into your sub-vi and use either the =93Bundle=94 or =93Bundle by Name=94 functio= n to write new data into the element. Bundle by Name will let you select which and how many of the cluster elements you want to write to. If you use the Bundle function, you must connect a value to each of the cluster elements on the function. So the Bundle by Name is usually the better way to go. Ed