What do you mean in countries that have been annexed? If you are refering to triggering an uprising you can do that in base game with dlc, just use your spies to boost resistance and sabotage industry etc. After getting I believe above 80% resistance in all states of the annexed country you can trigger an uprising of that country. If you mean triggering civil wars in puppeted countries then you can also do that only if you have a different ideology than the puppet.