Try disabling the Divided Loyalties mod, as I think that scews the Sith a bit sometimes. Or sometimes it's simply due to the unhappiness because you have to adjust the policies added from some mods.

The Sith want two things, war and slavery. And in general, an authoritarian state. However, there are some things like forced relocation that no pops like. And, if you want to ally with or even just not fight the Republic, they will war on you if you have too many 'evil' policies which they don't like.

You can use buildings like the virtual arena to raise happiness and habitability. And governors and rulers and government types.

As well as if you can afford the influence, you can use planetary edicts to temporarily raise happiness. I do agree though in my Sith AAR on the paradox forums you can see I had major rebellions. You need about 5 defensive garrisons per planet to handle things if a revolt does break out, as well as a 1000 point fleet and ten assault troops to attack the capital of a revolted faction if necessary.