How do you control the Rebel value? What does it influence? Does this affect happiness? Do I send them to therapy at the Centre, or the Dungeon for some torture?
Rebelliousness is influenced by a lot of things, Happiness, Tiredness, Love, Fear, Hate, if she is a slave or not (slaves have lower rebelliousness) and most importantly Obedience and Spirit.
You want high Obedience and low Spirit, low Spirit is less important than Obedience
Also several traits and items play into it (lowering or raising it) in an indirect way because they influence the stats above.
The most effective trait for it is Broken Will, which sets Rebelliousness to -100 no matter what else her stats say.
But that is not needed most of the time. A girl with Obedience and Love at max and low Hate values obeys you in most of the cases.
You can not directly influence Rebelliousness, because it is not an independent stat.
Rebelliousness is the result of the other stats, so Rebelliousness only influences if a girl does her job and how she performs or maybe tries to run away.
The Dungeon in itself does not do much, you need a girl as torturer in one of your brothels as well.
That increases (slow) Obedience and lowers Spirit for all girls in the dungeon but also lowers happiness, love and health and raises hate and fear.
It depends on your playstyle but i found the dungeon a bit inefficient because the happy loving slave approach is the most effective and while the Dungeon increases Obedience (which is good) it might take a while to get them to love you when you take them out of the dungeon.
Of course in this game the most effective approach are items (for almost everything).
A Brainwashing Oil combined with a Love Potion and you won't have problems.
Something that gets rid of the Broken Will as well, Psychologist Session (these are items) or a few turns with a counselor in the centre, because Broken Will can be bad.
Sometimes you want your whoring girls to fight back against aggressive customers.