Sorry, no. I haven't found a way to do this, if I want to manage it all from the primary CF instance. I can, of course, manipulate each instance independently. But that does rather defeat the purpose of having multiple instances via the Instance Manager.
I haven't looked in to it much more. I could probably hack together a combination of password-less sudo and editing of the coldfusion start/stop scripts. But I don't think that level of editing would be a good idea, not to mention if there ever is a CF update that might specifically rely on unaltered scripts.
PH