I'm looking to do something similar. My users would like to save the results of an Identify or Search query, so I just convert them to a FeatureLayer and it pops up in the TOC. After a few queries the TOC gets kinda large though, so I'd like to place them in a hierarchy by category. I can generate a blank FeatureLayer named "Identify Queries" and "Search Queries" that appears in the TOC, but unfortunately I see no way to attach sublayers to them.
Tony, one approach that may work is to define all of your operationallayers but use the Map Switcher <excludelayer> config option to hide them. That will load each layer but keep it off the TOC. Then in your event you can rename the desired layer so that it no longer matches the <excludelayer> entry, causing it to appear. It just might work.