When you have created a colony on a planet, you can modify most of the points you mentioned by the SM Mods button(colony window, third button from the right).
What you can't do is giving colonies from one player to another directly, as far as I know. But you can delete them at one population and create them at another(with the button above). You can also give troops or exchange techs. (troop and research tabs)
If you want the complete planet to rebel, abandon the former rulers colony then. But you can also have a civil war on the planet between the rebels and some loyalists.
Them only thing you can't change(or at least I don't know how) is the status of the population. It seems to be an imperial population all the time. If you want rioting pops, you have to conquer them first (=> 20% level of production, research, etc.).