You cannot use ArcSDE command line tools to add anything to a feature dataset, ever.
Tools written with just the ArcSDE API are not geodatabase-aware. Only ArcObjects-based
tools like ArcPy can manage feature dataset management.
I remember that registration has two phases, register with SDE and register with Geodatabase, and I never understand what the difference between them.
So, my question, if I want to write a python script to register with the geodatabase, which arcpy commands I can use?
and do I have to register it with SDE first?