Customized radio buttons is a neat idea I hadn't thought of. In my situation I dynamically load items into the subpanel and have no way of knowing until it runs, how many items there are that can be loaded into the subpanel. For me this is why I use a single column listbox listing the VIs that can be loaded and clicking on one loads it into the subpanel.
As for the question about control references. You could potentially scan through the subpanel VIs looking for the same references that you normally look for in the main. Or you could have events go the other way where the subpanel registers for all controls it has (similar to your Main right now) and then it can generate a user event sent to the Main with the reference of the control that just changed. This is just two of many different approaches and without knowing more its hard to say what would work best for you.